Energetic contribution of side chain hydrogen bonding to the stability of staphylococcal nuclease.


Abstract

Hydrogen bonds are a ubiquitous feature of protein structures, yet there is great uncertainty about the energetic contribution of hydrogen bonding to protein stability. This study addresses this question by making a series of single substitution mutations in the model protein staphylococcal nuclease. These mutants have had a residue capable of participating in hydrogen bonding either removed or introduced. The variants we have investigated are as follows: nine valines substituted with threonine and serine; eight threonines converted to valine, serine, and cysteine; and seven tyrosines replaced by phenylalanine and leucine. The stabilities of these 56 mutant proteins were determined by titration with guanidine hydrochloride using fluorescence as a probe of structure. In general, it was found that the stability effects of removing a hydrogen bonding residue and replacing it with a nonbonding residue were relatively small. This was true even in the case of buried residues participating in hydrogen bonds, where the substituted residue leaves an unfulfilled hydrogen bond in the hydrophobic core. In contrast, introducing a hydrogen bonding residue in place of a nonbonding residue was generally more costly energetically. A wide variability in the cost of burying a hydroxyl was observed, but this does not seem to be due to differences in hydrogen bonding. The overall energetic contribution of various wild-type hydrogen bonding interactions was evaluated as being favorable. A range of energies from approximately 1.5 to 4.0 kcal/mol was estimated for the contribution of these interactions to the stability of the native state. Study holds ProTherm entries: 4934, 4935, 4936, 4937, 4938, 4939, 4940, 4941, 4942, 4943, 4944, 4945, 4946, 4947, 4948, 4949, 4950, 4951, 4952, 4953, 4954, 4955, 4956, 4957, 4958, 4959, 4960, 4961, 4962, 4963, 4964, 4965, 4966, 4967, 4968, 4969, 4970, 4971, 4972, 4973, 4974, 4975, 4976, 4977, 4978, 4979, 4980, 4981, 4982, 4983, 4984, 4985, 4986, 4987, 4988, 4989, 4990, 5544, 7787, 7788, 7789, 7790, 7791, 7792, 7793, 7794, 7795, 7796, 7797, 7798, 7799, 7800, 7801, 7802, 7803, 7804, 7805, 7806, 7807, 7808, 7809, 7810, 7811, 7812, 7813, 7814, 7815, 7816, 7817, 7818, 7819, 7820, 7821, 7822, 7823, 7824, 7825, 7826, 7827, 7828, 7829, 7830, 7831, 7832, 7833, 7834, 7835, 7836, 7837, 7838, 7839, 7840, 7841, 7842 Extra Details: hydrogen bonds; valines; threonine; nonbonding residue;,buried residues; hydrophobic core

Submission Details

ID: KP8283u63

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:27 p.m.

Version: 1

Publication Details
Byrne MP;Manuel RL;Lowe LG;Stites WE,Biochemistry (1995) Energetic contribution of side chain hydrogen bonding to the stability of staphylococcal nuclease. PMID:7577991
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
3D8G 2008-05-23T00:00:00+0000 1.99 Crystal structure of Staphylococcal nuclease variant Delta+PHS I72R at cryogenic temperature
3QOJ 2011-02-10T00:00:00+0000 1.6 Cryogenic structure of Staphylococcal nuclease variant D+PHS/V23K
2OXP 2007-02-20T00:00:00+0000 2.0 Crystal Structure of Staphylococcal Nuclease mutant V66D/P117G/H124L/S128A
2LKV 2011-10-21T00:00:00+0000 0 Staphylococcal Nuclease PHS variant
3MVV 2010-05-04T00:00:00+0000 1.72 Crystal structure of Staphylococcal nuclease variant Delta+PHS F34A at cryogenic temperature
2M00 2012-10-14T00:00:00+0000 0 Solution structure of staphylococcal nuclease E43S mutant in the presence of ssDNA and Cd2+
3D4W 2008-05-15T00:00:00+0000 1.9 Crystal structure of Staphylococcal nuclease variant Delta+PHS A109R at cryogenic temperature
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
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

Relevant UniProtKB Entries

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