Core and surface mutations affect folding kinetics, stability and cooperativity in IL-1 beta: does alteration in buried water play a role?


Abstract

Interleukin-1 beta (IL-1 beta) is a cytokine and a member of the beta-trefoil superfamily of protein structures. An interesting feature in the folding of IL-1 beta, shared with some other members of the same topological family, is the existence of a slow step in folding to the native conformation from a discrete intermediate. Wanting to probe the nature of this slow step in the folding of WT IL-1 beta (tau(1)=45 seconds), we made ten sequence variants of IL-1 beta (L10A, T9Q, T9G, C8S, C8A, N7G, N7D, L6A, R4P, and R4Q), where all mutations are located along strand 1. This strand is not protected from hydrogen exchange until late in folding. Most of the mutations showed little effect on the kinetics of folding for IL-1 beta. However, C8 is clearly involved in both the late and the early steps in folding, while sequence variants at L10 and L6 affect only late events in folding. The value of the slowest relaxation time, tau(1), which is associated with the rate of native protein formation, increased for the refolding of C8S, while C8A, L6A, and L10A showed smaller but systematic increases in the value of tau(1.)For both C8S and C8A, the value of the step associated with formation of the intermediate, tau(2), was independent of denaturant concentration. In addition, mutations in the hydrophobic core (L10A, C8A, C8S, and L6A) and, surprisingly, along the surface (T9G, T9Q, and N7G) alter the stability. The most destabilizing mutations show changes in equilibrium unfolding cooperativity, which is atypical for destabilizing mutations in IL-1 beta. Crystallographic studies indicate that mutations along strand 1 may alter the number of ordered water molecules within the core. Thus, side-chain replacement in this region can disrupt essential main-chain interactions mediated by ordered water contacts in a highly cooperative network of hydrogen bonding. Study holds ProTherm entries: 10867, 10868, 10869, 10870, 10871, 10872, 10873, 10874, 10875, 10876, 10877 Extra Details: folding; stability; hydration; mutagenesis; beta-trefoil

Submission Details

ID: eUhdxf544

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:41 p.m.

Version: 1

Publication Details
Covalt JC;Roy M;Jennings PA,J. Mol. Biol. (2001) Core and surface mutations affect folding kinetics, stability and cooperativity in IL-1 beta: does alteration in buried water play a role? PMID:11254388
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
2KH2 2009-09-08 Solution structure of a scFv-IL-1B complex
7I1B 1992-10-15 HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF INTERLEUKIN-1 BETA IN SOLUTION BY THREE-AND FOUR-DIMENSIONAL NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
6I1B 1992-10-15 HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF INTERLEUKIN-1 BETA IN SOLUTION BY THREE-AND FOUR-DIMENSIONAL NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
5R8Q 2020-04-22 1.23 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z2643472210 in complex with INTERLEUKIN-1 BETA
5R7W 2020-04-22 1.27 PanDDA analysis group deposition of ground-state model of INTERLEUKIN-1 BETA
5R8E 2020-04-22 1.35 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z57475877 in complex with INTERLEUKIN-1 BETA
5R8M 2020-04-22 1.39 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z1818332938 in complex with INTERLEUKIN-1 BETA
5R8F 2020-04-22 1.41 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z2377835233 in complex with INTERLEUKIN-1 BETA
5R8O 2020-04-22 1.42 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z1881545321 in complex with INTERLEUKIN-1 BETA
5R8G 2020-04-22 1.43 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z1259086950 in complex with INTERLEUKIN-1 BETA
5R85 2020-04-22 1.44 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z1262246195 in complex with INTERLEUKIN-1 BETA
6Y8I 2020-06-17 1.46 Fragment KCL_I013 in complex with IL-1-beta
5R87 2020-04-22 1.47 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z44592329 in complex with INTERLEUKIN-1 BETA
5R8A 2020-04-22 1.47 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z1492796719 in complex with INTERLEUKIN-1 BETA
5R8D 2020-04-22 1.47 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z1745658474 in complex with INTERLEUKIN-1 BETA
5R8I 2020-04-22 1.47 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z210803634 in complex with INTERLEUKIN-1 BETA
5R8K 2020-04-22 1.47 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z355728146 in complex with INTERLEUKIN-1 BETA
5R88 2020-04-22 1.48 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z1545313172 in complex with INTERLEUKIN-1 BETA
5R8N 2020-04-22 1.48 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z57292400 in complex with INTERLEUKIN-1 BETA
5R8B 2020-04-22 1.49 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z2027049478 in complex with INTERLEUKIN-1 BETA
4GAI 2013-02-20 1.49 Crystal structure of EBI-005, a chimera of human IL-1beta and IL-1Ra
5R8H 2020-04-22 1.5 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z111716368 in complex with INTERLEUKIN-1 BETA
5R86 2020-04-22 1.5 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z943693514 in complex with INTERLEUKIN-1 BETA
5R8P 2020-04-22 1.53 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z818727262 in complex with INTERLEUKIN-1 BETA
2NVH 2006-12-12 1.53 Determination of Solvent Content in Cavities in Interleukin-1 Using Experimentally-Phased Electron Density
1L2H 2003-02-04 1.54 Crystal structure of Interleukin 1-beta F42W/W120F mutant
5R8C 2020-04-22 1.54 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z30857828 in complex with INTERLEUKIN-1 BETA
5R8L 2020-04-22 1.56 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z1891773393 in complex with INTERLEUKIN-1 BETA
5R8J 2020-04-22 1.62 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z355728146 in complex with INTERLEUKIN-1 BETA
5R89 2020-04-22 1.65 PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z217038356 in complex with INTERLEUKIN-1 BETA
3POK 2011-01-19 1.7 Interleukin-1-beta LBT L3 Mutant
4G6M 2012-12-19 1.81 Crystal structure of human IL-1beta in complex with therapeutic antibody binding fragment of gevokizumab
6Y8M 2020-03-18 1.9 Fragment bikinin bound to Interleukin 1 beta
1I1B 1990-01-15 2.0 CRYSTAL STRUCTURE OF RECOMBINANT HUMAN INTERLEUKIN-1BETA AT 2.0 ANGSTROMS RESOLUTION
4I1B 1990-04-15 2.0 FUNCTIONAL IMPLICATIONS OF INTERLEUKIN-1BETA BASED ON THE THREE-DIMENSIONAL STRUCTURE
2I1B 1990-04-15 2.0 CRYSTALLOGRAPHIC REFINEMENT OF INTERLEUKIN-1 BETA AT 2.0 ANGSTROMS RESOLUTION
1IOB 1996-08-17 2.0 INTERLEUKIN-1 BETA FROM JOINT X-RAY AND NMR REFINEMENT
4G6J 2012-12-19 2.03 Crystal structure of human IL-1beta in complex with the therapeutic antibody binding fragment of canakinumab
1TOO 2004-12-07 2.1 Interleukin 1B Mutant F146W
3LTQ 2011-02-16 2.1 Structure of Interleukin 1B solved by SAD using an inserted Lanthanide Binding Tag
5I1B 1992-01-15 2.1 A COMPARISON OF THE HIGH RESOLUTION STRUCTURES OF HUMAN AND MURINE INTERLEUKIN-1B
1TWE 2004-12-07 2.1 INTERLEUKIN 1 BETA MUTANT F101Y
1T4Q 2004-12-07 2.1 Interleukin 1 beta F101W
4GAF 2013-02-20 2.15 Crystal structure of EBI-005, a chimera of human IL-1beta and IL-1Ra, bound to human Interleukin-1 receptor type 1
5MVZ 2017-02-15 2.15 Fab 4AB007 bound to Interleukin-1-beta
5BVP 2015-09-02 2.2 The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta
1TP0 2005-02-08 2.2 Triple mutation in interleukin 1 beta cavity:replacement of phenylalanines with tryptophan.
1TWM 2004-12-07 2.26 Interleukin-1 Beta Mutant F146Y
9ILB 1999-01-06 2.28 HUMAN INTERLEUKIN-1 BETA
1S0L 2004-03-30 2.34 Interleukin 1 beta mutant F42W
1HIB 1994-01-31 2.4 THE STRUCTURE OF AN INTERLEUKIN-1 BETA MUTANT WITH REDUCED BIOACTIVITY SHOWS MULTIPLE SUBTLE CHANGES IN CONFORMATION THAT AFFECT PROTEIN-PROTEIN RECOGNITION
1ITB 1998-02-04 2.5 TYPE-1 INTERLEUKIN-1 RECEPTOR COMPLEXED WITH INTERLEUKIN-1 BETA
4DEP 2012-03-21 3.1 Structure of the IL-1b signaling complex
3O4O 2010-09-01 3.3 Crystal structure of an Interleukin-1 receptor complex

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
94.8 Interleukin-1 beta P46648 IL1B_CERAT
95.4 Interleukin-1 beta P79182 IL1B_MACFA
95.4 Interleukin-1 beta P51493 IL1B_MACNE
96.1 Interleukin-1 beta P48090 IL1B_MACMU
100.0 Interleukin-1 beta P01584 IL1B_HUMAN