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Design of Zn-Binding Peptide(s) from Protein Fragments
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SYSNO ASEP 0619174 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Design of Zn-Binding Peptide(s) from Protein Fragments Tvůrce(i) Kormaník, Ján Michael (UOCHB-X)
Herman, Daniel (UOCHB-X)
Andris, Erik (UOCHB-X) ORCID
Culka, Martin (UOCHB-X) ORCID
Gutten, Ondrej (UOCHB-X) RID, ORCID
Kožíšek, Milan (UOCHB-X) RID, ORCID
Bednárová, Lucie (UOCHB-X) RID, ORCID
Srb, Pavel (UOCHB-X) RID, ORCID
Veverka, Václav (UOCHB-X) RID, ORCID
Rulíšek, Lubomír (UOCHB-X) RID, ORCIDČíslo článku e202401014 Zdroj.dok. Chembiochem. - : Wiley - ISSN 1439-4227
Roč. 26, č. 7 (2025)Poč.str. 14 s. Jazyk dok. eng - angličtina Země vyd. US - Spojené státy americké Klíč. slova zinc(II) ; metal-binding peptide ; computer design ; isothermal calorimetry ; NMR ; QM modeling CEP GA23-05940S GA ČR - Grantová agentura ČR Výzkumná infrastruktura e-INFRA CZ II - 90254 - CESNET, zájmové sdružení právnických osob Způsob publikování Open access Institucionální podpora UOCHB-X - RVO:61388963 UT WOS 001432411900001 EID SCOPUS 85218882852 DOI https://doi.org/10.1002/cbic.202401014 Anotace We designed a minimalistic zinc(II)-binding peptide featuring the Cys(2)His(2) zinc-finger motif. To this aim, several tens of thousands of (His/Cys)-X-n-(His/Cys) protein fragments (n=2-20) were first extracted from the 3D protein structures deposited in Protein Data Bank (PDB). Based on geometrical constraints positioning two Cys (C) and two His (H) side chains at the vertices of a tetrahedron, approximately 22 000 sequences of the (H/C)-X-i-(H/C)-X-j-(H/C)-X-k-(H/C) type, satisfying Nmetal-binding H=Nmetal-binding C=2, were processed. Several other criteria, such as the secondary structure content and predicted fold stability, were then used to select the best candidates. To prove the viability of the computational design experimentally, three peptides were synthesized and subjected to isothermal calorimetry (ITC) measurements to determine the binding constants with Zn2+, including the entropy and enthalpy terms. For the strongest Zn2+ ions binding peptide, P1, the dissociation constant was shown to be in the nanomolar range (K-D=similar to 220 nM, corresponding to Delta G(bind)=-9.1 kcal mol(-1)). In addition, ITC showed that the [P1 : Zn2+] complex forms in 1 : 1 stoichiometry and two protons are released upon binding, which suggests that the zinc coordination involves both cysteines. NMR experiments also indicated that the structure of the [P1 : Zn2+] complex might be quite similar to the computationally predicted one. In summary, our proof-of-principle study highlights the usefulness of our computational protocol for designing novel metal-binding peptides. Pracoviště Ústav organické chemie a biochemie Kontakt asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Jana Procházková, Tel.: 220 183 418 Rok sběru 2026 Elektronická adresa https://doi.org/10.1002/cbic.202401014
Počet záznamů: 1