Enhancing the affinity of SEB-binding peptides by repeating their sequence

The utilization of peptide ligands in biosensors and bioassays is dependent on achieving high affinity of these peptides toward their targets. In a previous report, we identified 12-mer peptides that could selectively bind to Staphylococcal enterotoxin B (SEB) using a phage-display library. In this study, we explore for new modification approaches to enhance the affinity of two different SEB-binding peptides. In order to identify the binding regions of selected peptides, the charged residues and the ones, critical for the structure of peptide, were replaced with alanine. However, a specific binding region could not be suggested as all mutant peptides have lost their affinities toward SEB completely. The modifications for the affinity enhancement were done by repeating the 12-mer peptide sequences. A 10-fold increase was observed in the binding affinity of one of the two-repeated peptides, while this modification did not affect the affinity of the other tested peptide. The peptide, with enhanced affinity, was further modified as three repeats; however the affinity of the peptide decreased. The structural basis of the affinity difference between modified peptides was examined by molecular dynamics simulation. The results showed that the conformational differences hold the key for affinity of peptides modified by repeating the sequence. This high affinity peptide with increased affinity is a promising molecular recognition agent to be used in the detection of SEB to be utilized in biosensing systems. (C) 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 98: 145154, 2012.

Yazar Dudak, Fahriye Ceyda
Kilic, Nesrin
Demir, Kadir
Yasar, Fatih
Boyaci, Ismail Hakki
Yayın Türü Article
Tek Biçim Adres https://hdl.handle.net/20.500.12628/2549
Tek Biçim Adres 10.1002/bip.22012
Konu Başlıkları peptide ligands
phage display
isothermal titration calorimetry (ITC)
surface plasmon resonance (SPR)
Koleksiyonlar Araştırma Çıktıları | WoS | Scopus | TR-Dizin | PubMed | SOBİAD
PubMed İndeksli Yayınlar Koleksiyonu
WoS İndeksli Yayınlar Koleksiyonu
Dergi Adı BIOPOLYMERS
Dergi Cilt Bilgisi 98
Dergi Sayısı 2
Sayfalar 145 - 154
Yayın Yılı 2012
Eser Adı
[dc.title]
Enhancing the affinity of SEB-binding peptides by repeating their sequence
Yazar
[dc.contributor.author]
Dudak, Fahriye Ceyda
Yazar
[dc.contributor.author]
Kilic, Nesrin
Yazar
[dc.contributor.author]
Demir, Kadir
Yazar
[dc.contributor.author]
Yasar, Fatih
Yazar
[dc.contributor.author]
Boyaci, Ismail Hakki
Yayın Yılı
[dc.date.issued]
2012
Yayıncı
[dc.publisher]
WILEY
Yayın Türü
[dc.type]
article
Özet
[dc.description.abstract]
The utilization of peptide ligands in biosensors and bioassays is dependent on achieving high affinity of these peptides toward their targets. In a previous report, we identified 12-mer peptides that could selectively bind to Staphylococcal enterotoxin B (SEB) using a phage-display library. In this study, we explore for new modification approaches to enhance the affinity of two different SEB-binding peptides. In order to identify the binding regions of selected peptides, the charged residues and the ones, critical for the structure of peptide, were replaced with alanine. However, a specific binding region could not be suggested as all mutant peptides have lost their affinities toward SEB completely. The modifications for the affinity enhancement were done by repeating the 12-mer peptide sequences. A 10-fold increase was observed in the binding affinity of one of the two-repeated peptides, while this modification did not affect the affinity of the other tested peptide. The peptide, with enhanced affinity, was further modified as three repeats; however the affinity of the peptide decreased. The structural basis of the affinity difference between modified peptides was examined by molecular dynamics simulation. The results showed that the conformational differences hold the key for affinity of peptides modified by repeating the sequence. This high affinity peptide with increased affinity is a promising molecular recognition agent to be used in the detection of SEB to be utilized in biosensing systems. (C) 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 98: 145154, 2012.
Açıklama
[dc.description]
WOS: 000311339500007
Açıklama
[dc.description]
PubMed: 22733526
Kayıt Giriş Tarihi
[dc.date.accessioned]
2019-12-23
Açık Erişim Tarihi
[dc.date.available]
2019-12-23
Yayın Dili
[dc.language.iso]
eng
Konu Başlıkları
[dc.subject]
peptide ligands
Konu Başlıkları
[dc.subject]
phage display
Konu Başlıkları
[dc.subject]
isothermal titration calorimetry (ITC)
Konu Başlıkları
[dc.subject]
surface plasmon resonance (SPR)
Haklar
[dc.rights]
info:eu-repo/semantics/closedAccess
ISSN
[dc.identifier.issn]
0006-3525
ISSN
[dc.identifier.issn]
1097-0282
Sponsor YAYINCI
[dc.description.sponsorship]
Scientific and Technological Research Council of Turkey (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [108O031]; Hacettepe University Scientific Research FundHacettepe University [09.01.602.003]
Sponsor YAYINCI
[dc.description.sponsorship]
Contract grant sponsor: Scientific and Technological Research Council of Turkey (TUBITAK); Contract grant number: 108O031; Contract grant sponsor: Hacettepe University Scientific Research Fund; Contract grant number: 09.01.602.003
İlk Sayfa Sayısı
[dc.identifier.startpage]
145
Son Sayfa Sayısı
[dc.identifier.endpage]
154
Dergi Adı
[dc.relation.journal]
BIOPOLYMERS
Dergi Sayısı
[dc.identifier.issue]
2
Dergi Cilt Bilgisi
[dc.identifier.volume]
98
Tek Biçim Adres
[dc.identifier.uri]
https://dx.doi.org/10.1002/bip.22012
Tek Biçim Adres
[dc.identifier.uri]
https://hdl.handle.net/20.500.12628/2549
Görüntülenme Sayısı ( Şehir )
Görüntülenme Sayısı ( Ülke )
Görüntülenme Sayısı ( Zaman Dağılımı )
Görüntülenme
7
09.12.2022 tarihinden bu yana
İndirme
1
09.12.2022 tarihinden bu yana
Son Erişim Tarihi
18 Ekim 2023 13:11
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Tıklayınız
affinity peptides peptide modified binding modification repeating toward molecular 12-mer examined between difference structural decreased however observed repeats two-repeated further enhanced tested affect dynamics Biopolymers Periodicals 145154 systems biosensing utilized detection simulation recognition promising increased
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