Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.6
4.6
Journals
Molecules
Special Issues
Peptide and Protein Folding
molecules-logo
Submit to Special Issue Submit Abstract to Special Issue Review for Molecules Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Peptide and Protein Folding

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: 31 August 2026 | Viewed by 812

Special Issue Editors

Prof. Dr. Yuji Hidaka

E-Mail Website
Guest Editor
Faculty of Science and Engineering, Kindai University, Higashiosaka 577-8502, Japan
Interests: peptide and protein folding; peptide and protein science; disulfide bond formation; molecular evolution; chemical biology
Prof. Dr. Mahesh Narayan

E-Mail Website
Guest Editor
Department of Chemistry and Biochemistry, University of Texas at El Paso (UTEP), El Paso, TX 79968, USA
Interests: protein folding; docking; halogen bonding; reactive oxygen species; neurodegenerative disorders; drug-discovery; chemical education
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Michio Iwaoka

E-Mail Website
Guest Editor
Department of Chemistry, School of Science, Tokai University, Hiratsuka, Kanagawa, Japan
Interests: selenium chemistry; protein chemistry; weak atomic interactions; chiral acid; catalysts
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Understanding how peptides and proteins fold into their functional conformations remains a central challenge in Peptide and Protein Science. This Special Issue aims to provide a comprehensive overview of folding mechanisms, structural dynamics, and the molecular determinants that guide the correct formation of three-dimensional structures. We welcome studies exploring in vitro folding pathways, oxidative folding, disulfide bond formation, folding intermediates, and the development of innovative experimental or analytical approaches.

This Special Issue seeks both original research articles and reviews spanning peptide folding, protein folding mechanisms, misfolding and aggregation, stability engineering, refolding strategies, and methodological advances. By bringing together diverse insights from experimental, theoretical, and data-driven perspectives, we hope to highlight emerging concepts and stimulate new directions in the field. We encourage high-quality submissions from researchers working across biochemistry, structural biology, protein engineering, and related disciplines and look forward to hearing from you.

Prof. Dr. Yuji Hidaka
Prof. Dr. Mahesh Narayan
Prof. Dr. Michio Iwaoka
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • peptide structure and dynamics
  • disulfide bond formation
  • folding pathways and intermediates
  • protein stability and misfolding
  • machine learning in structural biology

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (1 paper)

Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

16 pages, 2563 KB  
Article
Structural and Catalytic Roles of the Disulfide Bonds Cys19–Cys154 and Cys134–Cys199 in Trypsin-like Proteases: Evolutionary Insights for Disulfide Bond Acquisition
by Maiko Minakata, Yuri Murakami, Orika Ashida, Miki Matsuzaki, Kairi Ogawa, Nanako Saeki, Shigeru Shimamoto, Mitsuhiro Miyazawa, Yuji Hidaka and Nana Sakata
Molecules 2026, 31(2), 351; https://doi.org/10.3390/molecules31020351 - 19 Jan 2026
Cited by 1 | Viewed by 534
Abstract
Trypsin is one of the most extensively studied enzymes in biochemistry. However, little information is available on the role of the disulfide bonds to establish the correct conformation and enzyme activity during molecular evolution. To obtain this information, two additional disulfide bonds corresponding [...] Read more.
Trypsin is one of the most extensively studied enzymes in biochemistry. However, little information is available on the role of the disulfide bonds to establish the correct conformation and enzyme activity during molecular evolution. To obtain this information, two additional disulfide bonds corresponding to those found in human trypsin were individually or simultaneously introduced into the trypsin-like protease cocoonase (Bombyx mori), which contains three consensus disulfide bonds, and structural effects were analyzed. Enzyme assays of the mutant proteins revealed that, during molecular evolution, the Cys19–Cys154 bond contributed to improving substrate recognition (Km), whereas the Cys134–Cys199 bond contributed to enhancing catalytic turnover (kcat). In addition, the Cys134–Cys199 disulfide bond significantly increased the structural stability, whereas the Cys19–Cys154 disulfide bond promoted a more compact folded ensemble. Interestingly, when both disulfide bridges were introduced together, their effects acted synergistically, yielding the highest catalytic activity toward the substrate BAEE (kcat/Km). Taken together, these findings suggest that trypsin-like proteases evolved through a two-step adaptive process: an initial phase in which the catalytic efficiency (kcat) and structural stability were enhanced, followed by a second phase in which the fold became more compact, thereby improving the overall enzymatic activity. Full article
(This article belongs to the Special Issue Peptide and Protein Folding)
►▼ Show Figures

Graphical abstract

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-1
Back to TopTop