Svoboda | Graniru | BBC Russia | Golosameriki | Facebook
 
 

Innovative Biotechnologies for Advancing Protein Function Investigation

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Biotechnology".

Deadline for manuscript submissions: 28 February 2025 | Viewed by 3567

Special Issue Editors


E-Mail Website
Guest Editor
School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172,China
Interests: NAD signaling; NAD-consuming enzyme; biochemistry; immunology; neurobiology; biotechnology

E-Mail Website
Guest Editor
1. Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
2. Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
Interests: molecular biology; cell biology; neurobiology; biochemistry; biotechnology; protein function; cell fate

E-Mail Website
Guest Editor
Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
Interests: molecular cell biology; biotechnology; protein interactions; gene expression and regulation; immunopathology

Special Issue Information

Dear Colleagues,

Proteins, as fundamental biomolecules, underpin a diverse array of cellular processes, forming the cornerstone of biological mechanisms. A comprehensive understanding of their functions is essential to elucidate biological mechanisms, unravel disease pathways, and facilitate therapeutic interventions. As our insight into protein function deepens, it is necessary to develop innovative biotechnological approaches, enabling us to interrogate protein functions with unprecedented precision and depth. This Special Issue aims to showcase pioneering research that introduces novel technologies, tools, and strategies to unravel the multifaceted functions of proteins across diverse biological systems.

The field of biotechnology has experienced a rapid evolution, from cutting-edge imaging modalities and high-throughput technologies to sophisticated computational models and precision protein engineering. These advancements have expanded our toolkit for investigating protein functions. This Special Issue builds upon this momentum, aiming to foster a deeper understanding of protein functions in a health and disease context.

We invite researchers, scientists, and experts in the field of biotechnology to contribute their original research, reviews, and perspectives to this Special Issue. Topics of interest include, but are not limited to:

  • Novel methodologies for achieving high-resolution visualization of proteins within intricate biological environments.
  • High-throughput screening technologies that facilitate the large-scale assessment of protein functions, expediting the identification of key functional players.
  • State-of-the-art computational models and algorithms, predicting protein functions, interactions, and dynamic structural changes.
  • Cutting-edge strategies designed to modify and optimize protein functions for specific applications.
  • Innovative tools and platforms designed to dissect complex protein–protein, protein–ligand interactions and signaling pathways.

This Special Issue bridges the gap between current literature and emerging biotechnological innovations, thus offering a unique and up-to-date perspective on the topic. While existing literature has undoubtedly contributed to our understanding of protein functions, this Special Issue distinguishes itself by focusing specifically on the latest technologies and strategies that drive our ability to scrutinize protein functions. It acknowledges the challenges and limitations faced by researchers in traditional protein studies and positions itself as a progressive extension of the current literature, offering a timely and comprehensive update on the state-of-the-art biotechnologies that are transforming protein function investigation.

Dr. Yongjuan Zhao
Dr. Wanhua Li
Dr. Qiwen Deng
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 100 words) can be sent to the Editorial Office for announcement on this website.

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. Biology is an international peer-reviewed open access monthly 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

  • protein imaging and visualization
  • high-throughput screening
  • computational methodologies
  • protein engineering
  • protein–protein interactions
  • protein–ligand interactions
  • biological mechanisms

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.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

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

Published Papers (4 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

24 pages, 6245 KiB  
Article
An In Silico Design of a Vaccine against All Serotypes of the Dengue Virus Based on Virtual Screening of B-Cell and T-Cell Epitopes
by Hikmat Ullah, Shaukat Ullah, Jinze Li, Fan Yang and Lei Tan
Biology 2024, 13(9), 681; https://doi.org/10.3390/biology13090681 - 30 Aug 2024
Viewed by 165
Abstract
Dengue virus poses a significant global health challenge, particularly in tropical and subtropical regions. Despite the urgent demand for vaccines in the control of the disease, the two approved vaccines, Dengvaxia and TV003/TV005, there are current questions regarding their effectiveness due to an [...] Read more.
Dengue virus poses a significant global health challenge, particularly in tropical and subtropical regions. Despite the urgent demand for vaccines in the control of the disease, the two approved vaccines, Dengvaxia and TV003/TV005, there are current questions regarding their effectiveness due to an increased risk of antibody-dependent enhancement (ADE) and reduced protection. These challenges have underscored the need for further development of improved vaccines for Dengue Virus. This study presents a new design using an in silico approach to generate a more effective dengue vaccine. Initially, our design process began with the collection of Dengue polyprotein sequences from 10 representative countries worldwide. And then conserved fragments of viral proteins were retrieved as the bases for epitope screening. The selection of epitopes was then carried out with criteria such as antigenicity, immunogenicity, and binding affinity with MHC molecules, while the exclusion criteria were according to their allergenicity, toxicity, and potential for antibody-dependent enhancement. We then constructed a core antigen with the selected epitopes and linked the outcomes with distinct adjuvant proteins, resulting in three candidate vaccines: PSDV-1, PSDV-2, and PSDV-3. Among these, PSDV-2 was selected for further validation due to its superior physicochemical and structural properties. Extensive simulations demonstrated that PSDV-2 exhibited strong binding to pattern recognition receptors, high stability, and robust immune induction, confirming its potential as a high-quality vaccine candidate. For its recombinant expression, a plasmid was subsequently designed. Our new vaccine design offers a promising additional option for Dengue virus protection. Further experimental validations will be conducted to confirm its protective efficacy and safety. Full article
Show Figures

Graphical abstract

14 pages, 8129 KiB  
Article
The Fluorinated NAD Precursors Enhance FK866 Cytotoxicity by Activating SARM1 in Glioblastoma Cells
by Wei Ming He, Jian Yuan Yang, Zhi Ying Zhao, Weimin Xiao, Wan Hua Li and Yong Juan Zhao
Biology 2024, 13(9), 649; https://doi.org/10.3390/biology13090649 - 23 Aug 2024
Viewed by 253
Abstract
Glioblastoma, a formidable brain tumor characterized by dysregulated NAD metabolism, poses a significant therapeutic challenge. The NAMPT inhibitor FK866, which induces NAD depletion, has shown promise in controlling tumor proliferation and modifying the tumor microenvironment. However, the clinical efficacy of FK866 as a [...] Read more.
Glioblastoma, a formidable brain tumor characterized by dysregulated NAD metabolism, poses a significant therapeutic challenge. The NAMPT inhibitor FK866, which induces NAD depletion, has shown promise in controlling tumor proliferation and modifying the tumor microenvironment. However, the clinical efficacy of FK866 as a single drug therapy for glioma is limited. In this study, we aim to disrupt NAD metabolism using fluorinated NAD precursors and explore their synergistic effect with FK866 in inducing cytotoxicity in glioblastoma cells. The synthesized analogue of nicotinamide riboside (NR), ara-F nicotinamide riboside (F-NR), inhibits nicotinamide ribose kinase (NRK) activity in vitro, reduces cellular NAD levels, and enhances FK866’s cytotoxicity in U251 glioblastoma cells, indicating a collaborative impact on cell death. Metabolic analyses reveal that F-NR undergoes conversion to fluorinated nicotinamide mononucleotide (F-NMN) and other metabolites, highlighting the intact NAD metabolic pathway in glioma cells. The activation of SARM1 by F-NMN, a potent NAD-consuming enzyme, is supported by the synergistic effect of CZ-48, a cell-permeable SARM1 activator. Temporal analysis underscores the sequential nature of events, establishing NAD depletion as a precursor to ATP depletion and eventual massive cell death. This study not only elucidates the molecular intricacies of glioblastoma cell death but also proposes a promising strategy to enhance FK866 efficacy through fluorinated NAD precursors, offering potential avenues for innovative therapeutic interventions in the challenging landscape of glioblastoma treatment. Full article
Show Figures

Figure 1

16 pages, 2756 KiB  
Article
Inhibition of Hyperglycemia and Hyperlipidemia by Blocking Toll-like Receptor 4: Comparison of Wild-Type and Toll-like Receptor 4 Gene Knockout Mice on Obesity and Diabetes Modeling
by Xingyu Zhao, Jiawei Zheng, Jing Wang, Bin Li and Wuyang Huang
Biology 2024, 13(1), 63; https://doi.org/10.3390/biology13010063 - 22 Jan 2024
Cited by 2 | Viewed by 1776
Abstract
Innate immune receptor TLR4 plays an important role in glycolipid metabolism. The objective of this study is to investigate the inhibitory effects of blocking TLR4 on hyperglycemia and hyperlipidemia by comparing WT and TLR4−/− mice in obesity and diabetes modeling. The knockout [...] Read more.
Innate immune receptor TLR4 plays an important role in glycolipid metabolism. The objective of this study is to investigate the inhibitory effects of blocking TLR4 on hyperglycemia and hyperlipidemia by comparing WT and TLR4−/− mice in obesity and diabetes modeling. The knockout of the TLR4 gene could prevent weight gain induced by a high-fat diet (HFD)/high-sugar and high-fat diet (HSHFD), and the differences in the responses existed between the sexes. It extends the time required to reach the obesity criteria. However, when mice were injected with intraperitoneal streptozotocin (STZ) after being fed by HSHFD for two months, TLR4−/− mice exhibited less weight loss than WT. Blocking TLR4 alleviated the changes in body weight and blood glucose, consequently reducing the efficiency of diabetes modeling, especially for male mice. Additionally, male TLR4−/− obese mice exhibit lower total cholesterol (TC) and low-density lipoprotein (LDL) levels in serum and less formation of fat droplets in the liver compared to WT. On the other hand, the knockout of TLR4 significantly increased the high-density lipoprotein (HDL) of male mice. This study should provide new insights into the role of TLR4, as well as opportunities to target novel approaches to the prevention and treatment of metabolic diseases like obesity and diabetes. Full article
Show Figures

Graphical abstract

Review

Jump to: Research

25 pages, 4907 KiB  
Review
Therapeutic Target Identification and Drug Discovery Driven by Chemical Proteomics
by Mingjie Zou, Haiyuan Zhou, Letian Gu, Jingzi Zhang and Lei Fang
Biology 2024, 13(8), 555; https://doi.org/10.3390/biology13080555 - 23 Jul 2024
Viewed by 951
Abstract
Throughout the human lifespan, from conception to the end of life, small molecules have an intrinsic relationship with numerous physiological processes. The investigation into small-molecule targets holds significant implications for pharmacological discovery. The determination of the action sites of small molecules provide clarity [...] Read more.
Throughout the human lifespan, from conception to the end of life, small molecules have an intrinsic relationship with numerous physiological processes. The investigation into small-molecule targets holds significant implications for pharmacological discovery. The determination of the action sites of small molecules provide clarity into the pharmacodynamics and toxicological mechanisms of small-molecule drugs, assisting in the elucidation of drug off-target effects and resistance mechanisms. Consequently, innovative methods to study small-molecule targets have proliferated in recent years, with chemical proteomics standing out as a vanguard development in chemical biology in the post-genomic age. Chemical proteomics can non-selectively identify unknown targets of compounds within complex biological matrices, with both probe and non-probe modalities enabling effective target identification. This review attempts to summarize methods and illustrative examples of small-molecule target identification via chemical proteomics. It delves deeply into the interactions between small molecules and human biology to provide pivotal directions and strategies for the discovery and comprehension of novel pharmaceuticals, as well as to improve the evaluation of drug safety. Full article
Show Figures

Figure 1

Back to TopTop