6B8R image
Entry Detail
PDB ID:
6B8R
Keywords:
Title:
Crystal structure of Staphylococcal nuclease variant Delta+PHS V23K/L36Q at cryogenic temperature
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2017-10-09
Release Date:
2017-10-18
Method Details:
Experimental Method:
Resolution:
1.65 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Thermonuclease
Mutations:V23K/L36Q/G50F/V51N/P117G/H124L/S128A/Del44-49
Chain IDs:A
Chain Length:143
Number of Molecules:1
Biological Source:Staphylococcus aureus
Primary Citation
Dielectric Properties of a Protein Probed by Reversal of a Buried Ion Pair.
J Phys Chem B 122 2516 2524 (2018)
PMID: 29466010 DOI: 10.1021/acs.jpcb.7b12121

Abstact

Thirty years ago, Hwang and Warshel suggested that a microenvironment preorganized to stabilize an ion pair would be incapable of reorganizing to stabilize the reverse ion pair. The implications were that (1) proteins have a limited capacity to reorganize, even under the influence of strong interactions, such as those present when ionizable groups are buried in the hydrophobic interior of a protein, and (2) the inability of proteins to tolerate the reversal of buried ion pairs demonstrates the limitations inherent to continuum electrostatic models of proteins. Previously we showed that when buried individually in the interior of staphylococcal nuclease, Glu23 and Lys36 have p K(a) values near pH 7, but when buried simultaneously, they establish a strong interaction of approximately 5 kcal/mol and have p K(a) values shifted toward more normal values. Here, using equilibrium thermodynamic measurements, crystal structures, and NMR spectroscopy experiments, we show that although the reversed, individual substitutions-Lys23 and Glu36-also have p K(a) values near 7, when buried together, they neither establish a strong interaction nor promote reorganization of their microenvironment. These experiments both confirm Warshel's original hypothesis and expand it by showing that it applies to reorganization, as demonstrated by our artificial ion pairs, as well as to preorganization as is commonly argued for motifs that stabilize naturally occurring ion pairs in polar microenvironments. These data constitute a challenging benchmark useful to test the ability of structure-based algorithms to reproduce the compensation between self-energy, Coulomb and polar interactions in hydrophobic environments of proteins.

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