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Molecular Recognition in Protein and Peptide Nanotechnology
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Molecular Recognition in Protein and Peptide Nanotechnology

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (30 December 2021) | Viewed by 21757

Special Issue Editors

Dr. Paško Konjevoda

E-Mail Website
Guest Editor
Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
Dr. Nikola Štambuk

E-Mail Website
Guest Editor
Centre for Nuclear Magnetic Resonance, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia

Special Issue Information

Dear Colleagues,

During the last four decades, a growing body of evidence has been accumulating on the specific interaction and molecular recognition of the complementary peptides, i.e., sense and antisense peptides specified by the complementary DNA and RNA sequences. The efficiency of this approach has been experimentally verified for more than 50 ligand–acceptor (receptor) systems, and it represents a promising field of research in biology and medicine. The interaction of sense and antisense peptides can be described with the set of rules combining physico-chemical properties of amino acids with bidirectional coding and stereochemical interaction. This natural genetic coding algorithm for complementary peptide interactions is neither expensive nor time-consuming, and enables simple and efficient design of interacting protein and peptide motifs. In combination to modern computational methods and database search, it represents a powerful new tool for the investigation and modeling of natural or de novo designed protein and peptide ligand-acceptor (receptor) systems.

Different applications include:

  1. Investigation of ligand and receptor structure, function and evolution
  2. Screening of protein and peptide ligands and acceptors (receptors)
  3. Development of vaccines, diagnostic tests and biomaterials
  4. Label-free technology to track drug candidates
  5. Peptidomimetics
  6. Investigation of peptide nucleic acids interaction

Dr. Paško Konjevoda
Dr. Nikola Štambuk
Guest Editors

Manuscript Submission Information

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Keywords

  • molecular recognition
  • complementary peptides
  • genetic coding algorithm
  • sense and antisense peptide binding
  • ligand and acceptor (receptor) modeling
  • label-fee visualisation technology
  • vaccines

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Published Papers (5 papers)

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Research

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13 pages, 402 KiB  
Article
Model of Genetic Code Structure Evolution under Various Types of Codon Reading
by Paweł Błażej, Konrad Pawlak, Dorota Mackiewicz and Paweł Mackiewicz
Int. J. Mol. Sci. 2022, 23(3), 1690; https://doi.org/10.3390/ijms23031690 - 1 Feb 2022
Cited by 1 | Viewed by 2045
Abstract
The standard genetic code (SGC) is a set of rules according to which 64 codons are assigned to 20 canonical amino acids and stop coding signal. As a consequence, the SGC is redundant because there is a greater number of codons than the [...] Read more.
The standard genetic code (SGC) is a set of rules according to which 64 codons are assigned to 20 canonical amino acids and stop coding signal. As a consequence, the SGC is redundant because there is a greater number of codons than the number of encoded labels. This redundancy implies the existence of codons that encode the same genetic information. The size and organization of such synonymous codon blocks are important characteristics of the SGC structure whose evolution is still unclear. Therefore, we studied possible evolutionary mechanisms of the codon block structure. We conducted computer simulations assuming that coding systems at early stages of the SGC evolution were sets of ambiguous codon assignments with high entropy. We included three types of reading systems characterized by different inaccuracy and pattern of codon recognition. In contrast to the previous study, we allowed for evolution of the reading systems and their competition. The simulations performed under minimization of translational errors and reduction of coding ambiguity produced the coding system resistant to these errors. The reading system similar to that present in the SGC dominated the others very quickly. The survived system was also characterized by low entropy and possessed properties similar to that in the SGC. Our simulation show that the unambiguous SGC could emerged from a code with a lower level of ambiguity and the number of tRNAs increased during the evolution. Full article
(This article belongs to the Special Issue Molecular Recognition in Protein and Peptide Nanotechnology)
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13 pages, 1198 KiB  
Article
Secondary Structures of Proteins Follow Menzerath–Altmann Law
by Vladimír Matlach, Daniel Dostál and Marian Novotný
Int. J. Mol. Sci. 2022, 23(3), 1569; https://doi.org/10.3390/ijms23031569 - 29 Jan 2022
Cited by 3 | Viewed by 2254
Abstract
This article examines the presence of the empirical tendency known as the Menzerath–Altmann Law (MAL) on protein secondary structures. MAL is related to optimization principles observed in natural languages and in genetic information on chromosomes or protein domains. The presence of MAL is [...] Read more.
This article examines the presence of the empirical tendency known as the Menzerath–Altmann Law (MAL) on protein secondary structures. MAL is related to optimization principles observed in natural languages and in genetic information on chromosomes or protein domains. The presence of MAL is examined on a non-redundant dataset of 4728 proteins by verifying significant, negative correlations and testing classical and newly proposed formulas by fitting the observed trend. We conclude that the lengths of secondary structures are specifically dependent on their number inside the protein sequence, while possibly reflecting the formula proposed in this paper. This behavior is observed on average but is individually avoidable and possibly driven by a latent cost function. The data suggest that MAL could provide a useful guiding principle in protein design. Full article
(This article belongs to the Special Issue Molecular Recognition in Protein and Peptide Nanotechnology)
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20 pages, 2779 KiB  
Article
Screening of Yeast Display Libraries of Enzymatically Treated Peptides to Discover Macrocyclic Peptide Ligands
by John Bowen, John Schneible, Kaitlyn Bacon, Collin Labar, Stefano Menegatti and Balaji M. Rao
Int. J. Mol. Sci. 2021, 22(4), 1634; https://doi.org/10.3390/ijms22041634 - 5 Feb 2021
Cited by 14 | Viewed by 5257
Abstract
We present the construction and screening of yeast display libraries of post-translationally modified peptides wherein site-selective enzymatic treatment of linear peptides is achieved using bacterial transglutaminase. To this end, we developed two alternative routes, namely (i) yeast display of linear peptides followed by [...] Read more.
We present the construction and screening of yeast display libraries of post-translationally modified peptides wherein site-selective enzymatic treatment of linear peptides is achieved using bacterial transglutaminase. To this end, we developed two alternative routes, namely (i) yeast display of linear peptides followed by treatment with recombinant transglutaminase in solution; or (ii) intracellular co-expression of linear peptides and transglutaminase to achieve peptide modification in the endoplasmic reticulum prior to yeast surface display. The efficiency of peptide modification was evaluated via orthogonal detection of epitope tags integrated in the yeast-displayed peptides by flow cytometry, and via comparative cleavage of putative cyclic vs. linear peptides by tobacco etch virus (TEV) protease. Subsequently, yeast display libraries of transglutaminase-treated peptides were screened to isolate binders to the N-terminal region of the Yes-Associated Protein (YAP) and its WW domains using magnetic selection and fluorescence activated cell sorting (FACS). The identified peptide cyclo[E-LYLAYPAH-K] featured a KD of 1.75 μM for YAP and 0.68 μM for the WW domains of YAP as well as high binding selectivity against albumin and lysozyme. These results demonstrate the usefulness of enzyme-mediated cyclization in screening combinatorial libraries to identify cyclic peptide binders. Full article
(This article belongs to the Special Issue Molecular Recognition in Protein and Peptide Nanotechnology)
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Review

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18 pages, 2172 KiB  
Review
Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research
by Nikola Štambuk, Paško Konjevoda and Josip Pavan
Int. J. Mol. Sci. 2021, 22(17), 9106; https://doi.org/10.3390/ijms22179106 - 24 Aug 2021
Cited by 5 | Viewed by 2945
Abstract
Antisense peptide technology (APT) is based on a useful heuristic algorithm for rational peptide design. It was deduced from empirical observations that peptides consisting of complementary (sense and antisense) amino acids interact with higher probability and affinity than the randomly selected ones. This [...] Read more.
Antisense peptide technology (APT) is based on a useful heuristic algorithm for rational peptide design. It was deduced from empirical observations that peptides consisting of complementary (sense and antisense) amino acids interact with higher probability and affinity than the randomly selected ones. This phenomenon is closely related to the structure of the standard genetic code table, and at the same time, is unrelated to the direction of its codon sequence translation. The concept of complementary peptide interaction is discussed, and its possible applications to diagnostic tests and bioengineering research are summarized. Problems and difficulties that may arise using APT are discussed, and possible solutions are proposed. The methodology was tested on the example of SARS-CoV-2. It is shown that the CABS-dock server accurately predicts the binding of antisense peptides to the SARS-CoV-2 receptor binding domain without requiring predefinition of the binding site. It is concluded that the benefits of APT outweigh the costs of random peptide screening and could lead to considerable savings in time and resources, especially if combined with other computational and immunochemical methods. Full article
(This article belongs to the Special Issue Molecular Recognition in Protein and Peptide Nanotechnology)
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16 pages, 303 KiB  
Review
Cancer Vaccines, Treatment of the Future: With Emphasis on HER2-Positive Breast Cancer
by Sandeep Pallerla, Ata ur Rahman Mohammed Abdul, Jill Comeau and Seetharama Jois
Int. J. Mol. Sci. 2021, 22(2), 779; https://doi.org/10.3390/ijms22020779 - 14 Jan 2021
Cited by 62 | Viewed by 8329
Abstract
Breast cancer is one of the leading causes of death in women. With improvements in early-stage diagnosis and targeted therapies, there has been an improvement in the overall survival rate in breast cancer over the past decade. Despite the development of targeted therapies, [...] Read more.
Breast cancer is one of the leading causes of death in women. With improvements in early-stage diagnosis and targeted therapies, there has been an improvement in the overall survival rate in breast cancer over the past decade. Despite the development of targeted therapies, tyrosine kinase inhibitors, as well as monoclonal antibodies and their toxin conjugates, all metastatic tumors develop resistance, and nearly one-third of HER2+ breast cancer patients develop resistance to all these therapies. Although antibody therapy has shown promising results in breast cancer patients, passive immunotherapy approaches have limitations and need continuous administration over a long period. Vaccine therapy introduces antigens that act on cancer cells causing prolonged activation of the immune system. In particular, cancer relapse could be avoided due to the presence of a longer period of immunological memory with an effective vaccine that can protect against various tumor antigens. Cancer vaccines are broadly classified as preventive and therapeutic. Preventive vaccines are used to ward off any future infections and therapeutic vaccines are used to treat a person with active disease. In this article, we provided details about the tumor environment, different types of vaccines, their advantages and disadvantages, and the current status of various vaccine candidates with a focus on vaccines for breast cancer. Current data indicate that therapeutic vaccines themselves have limitations in terms of efficacy and are used in combination with other chemotherapeutic or targeting agents. The majority of breast cancer vaccines are undergoing clinical trials and the next decade will see the fruitfulness of breast cancer vaccine therapy. Full article
(This article belongs to the Special Issue Molecular Recognition in Protein and Peptide Nanotechnology)
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