What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F24%3A00580275" target="_blank" >RIV/61388963:_____/24:00580275 - isvavai.cz</a>
Alternative codes found
RIV/00216208:11310/24:10478140
Result on the web
<a href="https://doi.org/10.1039/D3SC04960D" target="_blank" >https://doi.org/10.1039/D3SC04960D</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1039/d3sc04960d" target="_blank" >10.1039/d3sc04960d</a>
Alternative languages
Result language
angličtina
Original language name
What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments
Original language description
Certain peptide sequences, some of them as short as amino acid triplets, are significantly overpopulated in specific secondary structure motifs in folded protein structures. For example, 74% of the EAM triplet is found in alpha-helices, and only 3% occurs in the extended parts of proteins (typically beta-sheets). In contrast, other triplets (such as VIV and IYI) appear almost exclusively in extended parts (79% and 69%, respectively). In order to determine whether such preferences are structurally encoded in a particular peptide fragment or appear only at the level of a complex protein structure, NMR, VCD, and ECD experiments were carried out on selected tripeptides: EAM (denoted as pro-'alpha-helical' in proteins), KAM(alpha), ALA(alpha), DIC(alpha), EKF(alpha), IYI(pro-beta-sheet or more generally, pro-extended), and VIV(beta), and the reference alpha-helical CATWEAMEKCK undecapeptide. The experimental data were in very good agreement with extensive quantum mechanical conformational sampling. Altogether, we clearly showed that the pro-helical vs. pro-extended propensities start to emerge already at the level of tripeptides and can be fully developed at longer sequences. We postulate that certain short peptide sequences can be considered minimal “folding seeds“. Admittedly, the inherent secondary structure propensity can be overruled by the large intramolecular interaction energies within the folded and compact protein structures. Still, the correlation of experimental and computational data presented herein suggests that the secondary structure propensity should be considered as one of the key factors that may lead to understanding the underlying physico-chemical principles of protein structure and folding from the first principles.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Chemical Science
ISSN
2041-6520
e-ISSN
2041-6539
Volume of the periodical
15
Issue of the periodical within the volume
2
Country of publishing house
GB - UNITED KINGDOM
Number of pages
15
Pages from-to
594-608
UT code for WoS article
001119543500001
EID of the result in the Scopus database
2-s2.0-85179778467