Design of Zn-Binding Peptide(s) from Protein Fragments

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F25%3A00619174" target="_blank" >RIV/61388963:_____/25:00619174 - isvavai.cz</a>

Výsledek na webu

<a href="https://doi.org/10.1002/cbic.202401014" target="_blank" >https://doi.org/10.1002/cbic.202401014</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/cbic.202401014" target="_blank" >10.1002/cbic.202401014</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Design of Zn-Binding Peptide(s) from Protein Fragments

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Design of Zn-Binding Peptide(s) from Protein Fragments

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10403 - Physical chemistry

Projekt

<a href="/cs/project/GA23-05940S" target="_blank" >GA23-05940S: Katalytické metalopeptidy coby propojení světa nízkomolekulárních katalyzátorů a metaloenzymů</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2025

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Chembiochem

ISSN

1439-4227

e-ISSN

1439-7633

Svazek periodika

26

Číslo periodika v rámci svazku

7

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

14

Strana od-do

e202401014

Kód UT WoS článku

001432411900001

EID výsledku v databázi Scopus

2-s2.0-85218882852