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Biochemistry and Biophysics Tools for Peptide and Protein Research
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Biochemistry and Biophysics Tools for Peptide and Protein Research

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: 28 February 2027 | Viewed by 1755

Editor

Dr. Wenqi Li

E-Mail Website
Guest Editor
Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
Interests: bio-molecular preparation and characterization

Special Issue Information

Dear Colleagues,

We are pleased to invite you to contribute to this Special Issue entitled "Biochemistry and Biophysics Tools for Peptide and Protein Research." Peptides and proteins are fundamental to virtually every biological process, serving as key drivers of cellular function, signaling, and structural integrity. Understanding their structure, dynamics, interactions, and function is essential for advancing fields ranging from basic molecular biology to drug discovery and biotechnology. Recent years have witnessed remarkable progress in the development of cutting-edge biochemical and biophysical tools—spanning spectroscopic, computational, single-molecule, and high-throughput methodologies—that are transforming our ability to probe and manipulate peptides and proteins with unprecedented precision. This Special Issue seeks to highlight these innovative approaches, fostering interdisciplinary dialogue and accelerating discoveries in this dynamically evolving area.

This Special Issue aims to focus on cutting-edge technologies and methodological advancements in peptide and protein research, providing a platform for scholars to showcase innovative tools, technological applications, and interdisciplinary research.

In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following:

  • Application of biophysical tools in peptides and protein characterization;
  • Emerging techniques for protein structure and function analysis;
  • Dynamics and folding mechanisms of peptides and proteins;
  • Integrated computational and experimental methods for protein design;
  • High-throughput screening and single-molecule techniques in peptide research;
  • Advances in biomarker discovery and proteomics tools;
  • Interdisciplinary approaches in peptide-based drug development.

We look forward to receiving your contributions.

Dr. Wenqi Li
Guest Editor

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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • protein–protein interactions
  • peptide therapeutics development
  • biosensor and labeling technologies
  • high-throughput screening
  • mass spectrometry proteomics
  • protein dynamics and folding
  • single-molecule biophysics
  • analytical ultra-centrifugation
  • computational protein design
  • structural biology techniques

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

Published Papers (3 papers)

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Review

18 pages, 6508 KB  
Review
NMR Studies on Protein–Ligand Interactions
by Haiqin Yao and Ning Xu
Int. J. Mol. Sci. 2026, 27(17), 7561; https://doi.org/10.3390/ijms27177561 - 24 Aug 2026
Abstract
Protein–ligand interactions are fundamental to physiological processes and drug discovery. Based on the types of information on protein–ligand interactions provided by nuclear magnetic resonance (NMR) experiments, these NMR experiments can be categorized into three distinct classes: (i) molecular-level qualitative binding detection, (ii) residue-level [...] Read more.
Protein–ligand interactions are fundamental to physiological processes and drug discovery. Based on the types of information on protein–ligand interactions provided by nuclear magnetic resonance (NMR) experiments, these NMR experiments can be categorized into three distinct classes: (i) molecular-level qualitative binding detection, (ii) residue-level mapping of binding interfaces, and (iii) atomic-level structure determination and conformational dynamics of protein–ligand complexes. This hierarchy enables a workflow that accelerates the progression from initial binding identification to structural and dynamic characterization. In this review, we discuss how these experiments characterize molecular recognition. Notably, the term “ligand” in this article refers exclusively to small molecules. Full article
(This article belongs to the Special Issue Biochemistry and Biophysics Tools for Peptide and Protein Research)
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21 pages, 10851 KB  
Review
Analytical Ultracentrifugation for Biopharmaceutical Characterization and Quality Control
by Xiaojuan Yu, Wendan Chu, Qing Chang, Kaiyue Zhao, Zhaoxing Wang, Chengshi Zeng, Lan Wang, Chuanfei Yu and Wenqi Li
Int. J. Mol. Sci. 2026, 27(13), 6075; https://doi.org/10.3390/ijms27136075 - 7 Jul 2026
Viewed by 569
Abstract
Modern biotechnology has rapidly developed, and biotechnological drugs have become the center of global drug research and development as an important aspect of clinical treatment. These drugs have unique advantages, such as strong species specificity and prominent targeting, and they are widely used [...] Read more.
Modern biotechnology has rapidly developed, and biotechnological drugs have become the center of global drug research and development as an important aspect of clinical treatment. These drugs have unique advantages, such as strong species specificity and prominent targeting, and they are widely used in the treatment of various intractable diseases. However, their complex molecular structure, poor stability, and significant heterogeneity make quality control much more difficult than that of traditional small-molecule drugs that require high-precision analytical methods. Analytical ultracentrifugation (AUC) technology was pioneered by Theodor Svedberg during the early 20th century, and it has become an indispensable biophysical tool through technological innovation. This technology has unique advantages for the quality control of biotechnological drugs, including non-destructive detection, high resolution, and wide applicability. Therefore, AUC has been extensively adopted for the characterization of various biological products. This review systematically summarizes AUC technology applications in major categories of biotechnological drugs, with the aim to provide technical guidance and promote the standardized application of AUC. Full article
(This article belongs to the Special Issue Biochemistry and Biophysics Tools for Peptide and Protein Research)
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29 pages, 2051 KB  
Review
Navigating the Landscape of Cytometry-Based Single-Cell Proteomics: Quantification, Annotation, and Resources
by Yangbo Dai, Ziqiang Liu, Bing Liu, Li Guo, Huaicheng Sun and Qingxia Yang
Int. J. Mol. Sci. 2026, 27(8), 3620; https://doi.org/10.3390/ijms27083620 - 18 Apr 2026
Viewed by 643
Abstract
Cytometry-based single-cell proteomics (CySCP) has emerged as a powerful tool for analyzing cellular heterogeneity at the protein level because of its ability to reveal dynamic cell states and response patterns through high-dimensional protein expression profiling in thousands of individual cells. However, detailed summaries [...] Read more.
Cytometry-based single-cell proteomics (CySCP) has emerged as a powerful tool for analyzing cellular heterogeneity at the protein level because of its ability to reveal dynamic cell states and response patterns through high-dimensional protein expression profiling in thousands of individual cells. However, detailed summaries of quantification, processing and analysis of CySCP data remain limited. This review provides comprehensive perspectives on CySCP, including quantification technologies, analysis pipelines, annotation strategies, and resource platforms. Specifically, first, the strengths and limitations of the detection platforms are discussed. Second, comprehensive data processing steps, including compensation, transformation, normalization, batch effect correction, signal cleaning, and doublets, debris or dead cells removal, are described in detail. Third, various strategies for cell type annotation, including manual gating, unsupervised clustering, supervised/semi-supervised classification, and fully automated approaches, are illustrated. Fourth, emerging CySCP databases, as critical resources for facilitating antibody validation, panel optimization, and open-access data sharing, are summarized. In summary, this review provides a comprehensive guide for the use of CySCP to obtain novel biological insights at the single-cell protein level. Full article
(This article belongs to the Special Issue Biochemistry and Biophysics Tools for Peptide and Protein Research)
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