Energetics of side chain packing in staphylococcal nuclease assessed by systematic double mutant cycles.


Abstract

All 44 possible double mutant permutations of isoleucine, leucine, and valine were constructed in 11 pairings of six sites in the core of staphylococcal nuclease. The stabilities of these mutants were determined by guanidine hydrochloride denaturation. Comparison of the stabilities of all double mutants with those expected from addition of the corresponding single mutants showed that the effects of the two single mutations are energetically independent of each other in 30 of the double mutants. However, a substantial minority, 14, of the double mutants have stability effects that are not additive. In these cases, it appears that direct van der Waals contacts between the two side chains are present. The requirement of direct van der Waals contact for the interdependence of mutational stability effects is somewhat surprising in light of results previously reported by others. In addition, it was found that double mutants that did not alter or lower the overall number of atoms in the core and that showed nonadditive behavior were more stable than expected from addition of the effects of the corresponding single mutants. A net increase in the number of atoms in the core usually, but not always, resulted in a mutant that was less stable than expected. In contrast to previous staphylococcal nuclease double mutants, energetically significant changes to the denatured state do not appear to be occurring in these packing mutants. These conclusions imply that attempts to engineer protein stability based on single mutant data will be generally successful if overall core size is preserved and if residues are not in van der Waals contact. Study holds ProTherm entries: 12645, 12646, 12647, 12648, 12649, 12650, 12651, 12652, 12653, 12654, 12655, 12656, 12657, 12658, 12659, 12660, 12661, 12662, 12663, 12664, 12665, 12666, 12667, 12668, 12669, 12670, 12671, 12672, 12673, 12674, 12675, 12676, 12677, 12678, 12679, 12680, 12681, 12682, 12683, 12684, 12685, 12686, 12687, 12688 Extra Details: core; van der Waals contacts; packing mutants

Submission Details

ID: sW42py293

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:43 p.m.

Version: 1

Publication Details
Chen J;Stites WE,Biochemistry (2001) Energetics of side chain packing in staphylococcal nuclease assessed by systematic double mutant cycles. PMID:11705392
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
4WRD 2014-10-23T00:00:00+0000 1.65 Crystal structure of Staphylcoccal nulease variant Delta+PHS V66E L125E at cryogenic temperature
2LKV 2011-10-21T00:00:00+0000 0 Staphylococcal Nuclease PHS variant
2M00 2012-10-14T00:00:00+0000 0 Solution structure of staphylococcal nuclease E43S mutant in the presence of ssDNA and Cd2+
2OXP 2007-02-20T00:00:00+0000 2.0 Crystal Structure of Staphylococcal Nuclease mutant V66D/P117G/H124L/S128A
3D4W 2008-05-15T00:00:00+0000 1.9 Crystal structure of Staphylococcal nuclease variant Delta+PHS A109R at cryogenic temperature
3D8G 2008-05-23T00:00:00+0000 1.99 Crystal structure of Staphylococcal nuclease variant Delta+PHS I72R at cryogenic temperature
3MVV 2010-05-04T00:00:00+0000 1.72 Crystal structure of Staphylococcal nuclease variant Delta+PHS F34A at cryogenic temperature
3QOJ 2011-02-10T00:00:00+0000 1.6 Cryogenic structure of Staphylococcal nuclease variant D+PHS/V23K
3QOL 2011-02-10T00:00:00+0000 1.9 Crystal structure of Staphylococcal nuclease variant D+PHS/V23E at pH 6 determined at 100 K
3R3O 2011-03-16T00:00:00+0000 1.9 Crystal structure of Staphylococcal nuclease variant Delta+PHS T62A at cryogenic temperature and with high redundancy

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Thermonuclease P00644 NUC_STAAU
99.3 Thermonuclease Q5HHM4 NUC_STAAC
99.1 Thermonuclease Q99VJ0 NUC_STAAM
99.1 Thermonuclease Q7A6P2 NUC_STAAN
99.3 Thermonuclease Q6GB41 NUC_STAAS
99.3 Thermonuclease Q8NXI6 NUC_STAAW
99.3 Thermonuclease Q6GIK1 NUC_STAAR