Thermodynamic and structural compensation in "size-switch" core repacking variants of bacteriophage T4 lysozyme.


Abstract

Previous analysis of randomly generated multiple mutations within the core of bacteriophage T4 lysozyme suggested that the "large-to-small" substitution Leu121 to Ala (L121A) and the spatially adjacent "small-to-large" substitution Ala129 to Met (A129M) might be mutually compensating. To test this hypothesis, the individual variants L121A and A129M were generated, as well as the double "size-switch" mutant L121A/A129M. To make the interchange symmetrical, the combination of L121A with A129L to give L121A/A129L was also constructed. The single mutations were all destabilizing. Somewhat surprisingly, the small-to-large substitutions, which increase hydrophobic stabilization but can also introduce strain, were less deleterious than the large-to-small replacements. Both Ala129 --> Leu and Ala129 --> Met offset the destabilization of L121A by about 50%. Also, in contrast to typical Leu --> Ala core substitutions, which destabilize by 2 to 5 kcal/mol, Leu121 --> Ala slightly stabilized A129L and A129M. Crystal structure analysis showed that a combination of side-chain and backbone adjustments partially accommodated changes in side-chain volume, but only to a limited degree. For example, the cavity that was created by the Leu121 to Ala replacement actually became larger in L121A/A129L. The results demonstrate that the destabilization associated with a change in volume of one core residue can be specifically compensated by an offsetting volume change in an adjacent residue. It appears, however, that complete compensation is unlikely because it is difficult to reconstitute an equivalent set of interactions. The relatively slow evolution of core relative to surface residues appears, therefore, to be due to two factors. First, a mutation in a single core residue that results in a substantial change in size will normally lead to a significant loss in stability. Such mutations will presumably be selected against. Second, if a change in bulk does occur in a buried residue, it cannot normally be fully compensated by a mutation of an adjacent residue. Thus, the most probable response will tend to be reversion to the parent protein. Study holds ProTherm entries: 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1120, 13528, 13529, 13530, 13531, 13532, 13533, 13534 Extra Details: cysteine-free pseudo wild type lysozyme, 1L63 (C54T, C97A) correlated mutations; hydrophobic core; packing mutants;,intragenic suppressor; coordinated substitutions

Submission Details

ID: AUbAhceW4

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:16 p.m.

Version: 1

Publication Details
Baldwin E;Xu J;Hajiseyedjavadi O;Baase WA;Matthews BW,J. Mol. Biol. (1996) Thermodynamic and structural compensation in "size-switch" core repacking variants of bacteriophage T4 lysozyme. PMID:8676387
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
3EML 2008-09-24T00:00:00+0000 2.6 The 2.6 A Crystal Structure of a Human A2A Adenosine Receptor bound to ZM241385.
3SB8 2011-06-03T00:00:00+0000 2.65 Cu-mediated Dimer of T4 Lysozyme D61H/K65H by Synthetic Symmetrization
5JWW 2016-05-12T00:00:00+0000 1.47 T4 Lysozyme L99A/M102Q with 1-Hydro-2-ethyl-1,2-azaborine Bound
3SB9 2011-06-03T00:00:00+0000 2.45 Cu-mediated Dimer of T4 Lysozyme R76H/R80H by Synthetic Symmetrization
5YQR 2017-11-07T00:00:00+0000 2.4 Crystal structure of the PH-like domain of Lam6
1CTW 1999-08-20T00:00:00+0000 2.1 T4 LYSOZYME MUTANT I78A
3SN6 2011-06-28T00:00:00+0000 3.2 Crystal structure of the beta2 adrenergic receptor-Gs protein complex
2RBQ 2007-09-19T00:00:00+0000 1.63 3-methylbenzylazide in complex with T4 L99A/M102Q
1T8F 2004-05-12T00:00:00+0000 2.15 Crystal structure of phage T4 lysozyme mutant R14A/K16A/I17A/K19A/T21A/E22A/C54T/C97A
3CDV 2008-02-27T00:00:00+0000 1.73 Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Endolysin P00720 ENLYS_BPT4