Foldameric miniproteins - structure and catalytic function

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Principal Investigator: Łukasz Berlicki

Team:

Dr. hab. Ewa Rudzińska-Szostak

Dr. Barbara Barycza (2017-18)

Dr. Magda Drewniak (2017-19)

Dr. Katarzyna Ożga

Dr. Jeelan Shaik (2019-20)

Paweł Morawiak (PhD student)

Juan Lizandra Perez (PhD student)

Karolina Bogacka (MSc student)

Aleksandra Nielsen (MSc student)


Project financed by National Science Centre, no 2016/21/B/ST5/00269

Start date: February 2nd, 2017

Project duration: 45 months

Budget: 1 623 100 PLN

Abstract

Foldamers are oligomers with a strong tendency to form well-defined three-dimensional structures in solution. They constitute a field of science that has grown rapidly in recent years due to the numerous exciting features of such molecules. One of the most widely studied branches of this research concerns peptides with incorporated beta-amino acid residues. The mimicking of native secondary structures (in particular helices) has been the main focus until now. The possibility of the rational structural design of peptidic foldamers has led to the discovery of compounds showing desirable properties, such as inhibitors of protein-protein interactions for cancer treatment.

This research proposal is related to studies on foldamers that will be able to form protein-like three-dimensional structures. Basing on known alpha-peptidic mini-protein templates and the toolbox of previously studied foldameric secondary structures, we plan to present a rational strategy for the construction of extended protein-like foldameric structures (foldameric mini-proteins). Subsequently, we plan to use the discovered scaffolds for the development of enzyme mimetics. The grafting of the chosen enzyme active sites on elaborated molecular architectures will lead to catalytically active molecules. Four enzyme classes (metallohydrolases, serine hydrolases, aldolases and epoxide hydrolases) are planned to be mimicked.

The possibility of rational construction of structurally extended molecules gives chance to develop materials with various functionalities. In particular, development of molecules with chosen catalytic activity could be of high importance for a wide range of scientific fields. Importantly, the proposed methodology of artificial enzyme construction shows numerous advantages in comparison to other approaches (rational design, efficient synthetic methods, possibility structural studies by CD and NMR spectroscopies). We hope that studies on peptidic foldamers will give an insight into the rules governing the construction of the native proteins, in particular enzymes.


Press releases

ECHO24 TV

Conference communications

  1. M. Drewniak, Ł. Berlicki, "Controlling the conformational stability of helix-loop-helix peptide foldamers", 24th Polish Peptide Symposium, Jastrzębia Góra, 2017.
  2. K. Ożga, Ł. Berlicki, "Alpha,beta-peptidic foldamers with aldolase-like activity", 24th Polish Peptide Symposium, Jastrzębia Góra, 2017.
  3. P. Morawiak, , Ł. Berlicki, "Trimerisation of peptides containing beta-aminocyclopentanecarboxylic acid residues", 24th Polish Peptide Symposium, Jastrzębia Góra, 2017.
  4. Ł. Berlicki, M. Szefczyk, E. Węglarz-Tomczak, M. Drewniak, K ożga, A. Krzysztoń, E. Rudzińska-Szostak, J. Krzciuk-Gula, "Catalytically active peptide foldamers", 25th American Peptide Symposium, Whistler, 2017.
  5. M. Drewniak, K. Ożga, E. Rudzińska-Szostak, Ł. Berlicki "The conformational stability of helix-loop-helix peptide foldamers", 25th American Peptide Symposium, Whistler, 2017.
  6. Ł. Berlicki, M. Drewniak, K. Ożga, P. Morawiak, B. Barycza, P. Fortuna, E. Rudzińska-Szostak, "Foldameric mini-proteins - structure and catalytic activity", 10th International Peptide Symposium, Kyoto 2018 - poster.
  7. K. Ożga, Ł. Berlicki, "Peptidic foldamers as promising scaffolds for incorporation of enzymatic activity", 10th International Peptide Symposium, Kyoto 2018.
  8. Ł. Berlicki, "Structure and catalytic activity of de novo designed miniproteins", 25th Polish Peptide Symposium, Wojanów 2019.
  9. P. Morawiak, Ł. Berlicki "Rational design of cysteine protease peptide mimetics", 25th Polish Peptide Symposium, Wojanów 2019.
  10. K. Ożga, Ł. Berlicki, "Artificial aldolases based on miniprotein scaffold", 25th Polish Peptide Symposium, Wojanów 2019.

Publications

  • Ożga, K.; Berlicki, Ł., Design and Engineering of Miniproteins ACS Bio Med Chem Au 2022, 2, 316. View at Publisher
    Abstract
    The potential of miniproteins in the biological and chemical sciences is constantly increasing. Significant progress in the design methodologies has been achieved over the last 30 years. Early approaches based on propensities of individual amino acid residues to form individual secondary structures were subsequently improved by structural analyses using NMR spectroscopy and crystallography. Consequently, computational algorithms were developed, which are now highly successful in designing structures with accuracy often close to atomic range. Further perspectives include construction of miniproteins incorporating non-native secondary structures derived from sequences with units other than α-amino acids. Noteworthy, miniproteins with extended structures, which are now feasibly accessible, are excellent scaffolds for construction of functional molecules..
  • Drewniak, M.; Barycza, B.; Rudzińska-Szostak, E.; Morawiak, P.; Berlicki, Ł., Constrained beta-amino acid-containing miniproteins Org. Biomol. Chem. 2021, 19, 4272. View at Publisher
    Abstract

    The construction of beta-amino acid-containing peptides that fold to tertiary structures in solution remains challenging. Two model miniproteins, namely, Trp-cage and FSD, were scanned using constrained beta-amino acid in order to evaluate its impact on the folding process. Relationships between forces stabilizing miniprotein structure and conformational stability of analogues were found. The possibility of significant increase of a conformational stability of studied miniproteins by substitution with beta-amino acid at terminus of a helix was shown. On the basis of these results, beta-amino acid containing-peptide analogs with helical fragments substantially altered by incorporation of several constrained beta-amino acids were designed, synthesized and evaluated with respect to their structure and stability. The smallest known -amino acid-containing peptide with well-defined tertiary structure is described..
  • Ożga, K.; Drewniak-Świtalska, M.; Rudzińska-Szostak, E.; Berlicki, Ł., Towards Foldameric Miniproteins: A Helix‐Turn‐Helix Motif ChemPlusChem 2021, 86, 646. View at Publisher
    Abstract

    Numerous beta‐amino acid containing peptides forming secondary structures have been already described, however the design of higher order structures remains poorly explored. The methodology allowing construction of sequence patterns containing few rigid secondary element was proposed and experimentally validated. On a basis of 9/10/9/12‐helix containing cis‐2‐aminocyclopentanecarboxylic acid (cis‐ACPC) residues arranged in aabb sequence pattern, a conformationally stable helix‐turn‐helix structure was designed. The connection between two helices was also constructed using cis‐ACPC residues. Five examples of designed peptides were obtained and analyzed using circular dichroism and nuclear magnetic resonance spectroscopies, which confirmed the assumed way of folding. The NMR structure was calculated for the peptide with the highest number of non‐sequential contacts..
  • Bejger, M.; Fortuna, P.; Drewniak, M.; Plewka, J.; Rypniewski, W.; Berlicki, Ł., A computationally designed β-amino acid-containing miniprotein. Chem. Commun. 2021, 57, 6015. View at Publisher
    Abstract

    A new miniprotein built from three helices, including one structure based on a ααβαααβ sequence pattern was developed. Its crystal structure revealed a compact conformation with a well-packed hydrophobic core of unprecedented structure. The miniprotein formed dimers that were stabilized by an interaction of the hydrophobic surfaces..