-
Something wrong with this record ?
Protein-Ligand Interactions in the STING Binding Site Probed by Rationally Designed Single-Point Mutations: Experiment and Theory
Z. Vavřina, O. Gutten, M. Smola, M. Zavřel, Z. Aliakbar Tehrani, V. Charvát, M. Kožíšek, E. Boura, G. Birkuš, L. Rulíšek
Language English Country United States
Document type Journal Article, Research Support, Non-U.S. Gov't
- MeSH
- Point Mutation * MeSH
- Protein Conformation MeSH
- Crystallography, X-Ray MeSH
- Humans MeSH
- Membrane Proteins chemistry genetics metabolism MeSH
- Molecular Structure MeSH
- Nucleotides, Cyclic chemistry metabolism MeSH
- Protein Domains MeSH
- Binding Sites MeSH
- Hydrogen Bonding MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
STING protein (stimulator of interferon genes) plays an important role in the innate immune system. A number of potent compounds regulating its activity have been reported, mostly derivatives of cyclic dinucleotides (CDNs), natural STING agonists. Here, we aim to provide complementary information to large-scale "ligand-profiling" studies by probing the importance of STING-CDN protein-ligand interactions on the protein side. We examined in detail six typical CDNs each in complex with 13 rationally devised mutations in STING: S162A, S162T, Y167F, G230A, R232K, R232H, A233L, A233I, R238K, T263A, T263S, R293Q, and G230A/R293Q. The mutations switch on and off various types of protein-ligand interactions: π-π stacking, hydrogen bonding, ionic pairing, and nonpolar contacts. We correlated experimental data obtained by differential scanning fluorimetry, X-ray crystallography, and isothermal titration calorimetry with theoretical calculations. This enabled us to provide a mechanistic interpretation of the differences in the binding of representative CDNs to STING. We observed that the G230A mutation increased the thermal stability of the protein-ligand complex, indicating an increased level of ligand binding, whereas R238K and Y167F led to a complete loss of stabilization (ligand binding). The effects of the other mutations depended on the type of ligand (CDN) and varied, to some extent. A very good correlation (R2 = 0.6) between the experimental binding affinities and interaction energies computed by quantum chemical methods enabled us to explain the effect of the studied mutations in detail and evaluate specific interactions quantitatively. Our work may inspire development of high-affinity ligands against the common STING haplotypes by targeting the key (sometimes non-intuitive) protein-ligand interactions.
References provided by Crossref.org
- 000
- 00000naa a2200000 a 4500
- 001
- bmc21019104
- 003
- CZ-PrNML
- 005
- 20230519085131.0
- 007
- ta
- 008
- 210728s2021 xxu f 000 0|eng||
- 009
- AR
- 024 7_
- $a 10.1021/acs.biochem.0c00949 $2 doi
- 035 __
- $a (PubMed)33586948
- 040 __
- $a ABA008 $b cze $d ABA008 $e AACR2
- 041 0_
- $a eng
- 044 __
- $a xxu
- 100 1_
- $a Vavřina, Zdeněk $u Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic $u Department of Biochemistry, Faculty of Science, Charles University, Prague 110 00, Czech Republic
- 245 10
- $a Protein-Ligand Interactions in the STING Binding Site Probed by Rationally Designed Single-Point Mutations: Experiment and Theory / $c Z. Vavřina, O. Gutten, M. Smola, M. Zavřel, Z. Aliakbar Tehrani, V. Charvát, M. Kožíšek, E. Boura, G. Birkuš, L. Rulíšek
- 520 9_
- $a STING protein (stimulator of interferon genes) plays an important role in the innate immune system. A number of potent compounds regulating its activity have been reported, mostly derivatives of cyclic dinucleotides (CDNs), natural STING agonists. Here, we aim to provide complementary information to large-scale "ligand-profiling" studies by probing the importance of STING-CDN protein-ligand interactions on the protein side. We examined in detail six typical CDNs each in complex with 13 rationally devised mutations in STING: S162A, S162T, Y167F, G230A, R232K, R232H, A233L, A233I, R238K, T263A, T263S, R293Q, and G230A/R293Q. The mutations switch on and off various types of protein-ligand interactions: π-π stacking, hydrogen bonding, ionic pairing, and nonpolar contacts. We correlated experimental data obtained by differential scanning fluorimetry, X-ray crystallography, and isothermal titration calorimetry with theoretical calculations. This enabled us to provide a mechanistic interpretation of the differences in the binding of representative CDNs to STING. We observed that the G230A mutation increased the thermal stability of the protein-ligand complex, indicating an increased level of ligand binding, whereas R238K and Y167F led to a complete loss of stabilization (ligand binding). The effects of the other mutations depended on the type of ligand (CDN) and varied, to some extent. A very good correlation (R2 = 0.6) between the experimental binding affinities and interaction energies computed by quantum chemical methods enabled us to explain the effect of the studied mutations in detail and evaluate specific interactions quantitatively. Our work may inspire development of high-affinity ligands against the common STING haplotypes by targeting the key (sometimes non-intuitive) protein-ligand interactions.
- 650 _2
- $a vazebná místa $7 D001665
- 650 _2
- $a krystalografie rentgenová $7 D018360
- 650 _2
- $a lidé $7 D006801
- 650 _2
- $a vodíková vazba $7 D006860
- 650 _2
- $a membránové proteiny $x chemie $x genetika $x metabolismus $7 D008565
- 650 _2
- $a molekulární struktura $7 D015394
- 650 _2
- $a nukleotidy cyklické $x chemie $x metabolismus $7 D009712
- 650 12
- $a bodová mutace $7 D017354
- 650 _2
- $a konformace proteinů $7 D011487
- 650 _2
- $a proteinové domény $7 D000072417
- 655 _2
- $a časopisecké články $7 D016428
- 655 _2
- $a práce podpořená grantem $7 D013485
- 700 1_
- $a Gutten, Ondrej $u Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
- 700 1_
- $a Smola, Miroslav $u Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
- 700 1_
- $a Zavřel, Martin $u Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
- 700 1_
- $a Aliakbar Tehrani, Zahra $u Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic $u Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec 252 50, Czech Republic
- 700 1_
- $a Charvát, Vilém $u Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
- 700 1_
- $a Kožíšek, Milan $u Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
- 700 1_
- $a Boura, Evzen $u Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
- 700 1_
- $a Birkuš, Gabriel, $u Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic $d 1972- $7 xx0301324
- 700 1_
- $a Rulíšek, Lubomír $u Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
- 773 0_
- $w MED00009310 $t Biochemistry $x 1520-4995 $g Roč. 60, č. 8 (2021), s. 607-620
- 856 41
- $u https://pubmed.ncbi.nlm.nih.gov/33586948 $y Pubmed
- 910 __
- $a ABA008 $b sig $c sign $y p $z 0
- 990 __
- $a 20210728 $b ABA008
- 991 __
- $a 20230519085124 $b ABA008
- 999 __
- $a ok $b bmc $g 1690024 $s 1139550
- BAS __
- $a 3
- BAS __
- $a PreBMC
- BMC __
- $a 2021 $b 60 $c 8 $d 607-620 $e 20210215 $i 1520-4995 $m Biochemistry (Easton) $n Biochemistry $x MED00009310
- LZP __
- $a Pubmed-20210728
