tools, such as molecular docking, are widely applied to study interactions and binding affinity of biological activity of proteins and peptides. However, restricted sampling of both ligand and receptor conformations and use of approximated scoring functions can produce results that do not correlate with actual experimental binding affinities. Molecular dynamics simulations (MDS) can provide valuable information in deciphering functional mechanisms of proteins/peptides and other biomolecules, overcoming the rigid sampling limitations in docking analysis. This review will discuss the information related to the traditional use of models, such as molecular docking, and its application for studying food proteins and bioactive peptides, followed by an in-depth introduction to the theory of MDS and description of why these molecular simulation techniques are important in the theoretical prediction of structural and functional dynamics of food proteins and bioactive peptides. Applications, limitations, and future prospects of MDS will also be discussed.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/acs.jafc.1c06110 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Acetylshikonin Derived From Arnebia euchroma (Royle) Johnst Kills Multidrug-Resistant Gram-Positive Pathogens In Vitro and In Vivo.
Phytother Res
January 2025
College of Veterinary Medicine, Yangzhou University, Yangzhou, China.
The rising prevalence of multidrug-resistant (MDR) Gram-positive bacteria threatens the effectiveness of current antibiotic therapies. However, the development of new antibiotics has stagnated in recent years, highlighted the critical need for the discovery of innovative antimicrobial agents. This study aims to evaluate the antibacterial activity of naphthoquinones derived from Arnebia euchroma (Royle) Johnst (ADNs) and elucidate their underlying mechanisms.
View Article and Find Full Text PDFInvestigation of Anti-Apoptotic Effects and Mechanisms of Astragaloside IV in a Rat Model of Cerebral Ischemia-Reperfusion Injury.
CNS Neurosci Ther
January 2025
Qingshan Lake Science and Technology Innovation Center, Hangzhou Medical College, Hangzhou, China.
Background: Ischemic stroke is a prevalent and life-threatening cerebrovascular disease that is challenging to treat and associated with a poor prognosis. Astragaloside IV (AS-IV), a primary bioactive component of Astragali radix, has demonstrated neuroprotective benefits in previous studies. This study aimed to explore the mechanisms through which AS-IV may treat cerebral ischemia-reperfusion injury (CIRI).
View Article and Find Full Text PDFSPI1 facilitates microfracture-mediated cartilage regeneration in the elderly by enhancing bone marrow stromal cells ctemness.
J Tissue Eng
January 2025
Department of Sports Medicine and Joint Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.
Bone marrow stimulation treatment by bone marrow stromal cells (BMSCs) released from the bone medullary cavity and differentiated into cartilage via microfracture surgery is a frequently employed technique for treating articular cartilage injuries, yet the treatment presents a main drawback of poor cartilage regeneration in the elderly. Prior research indicated that aging could decrease the stemness capacity of BMSCs, thus we made a hypothesis that increasing old BMSCs (OBMSCs) stemness might improve the results of microfracture in the elderly. First, we investigated the correlation between microfracture outcomes and BMSCs stemness using clinical data and animal experiments.
View Article and Find Full Text PDFElucidating the mechanism of stigmasterol in acute pancreatitis treatment: insights from network pharmacology and / experiments.
Front Pharmacol
December 2024
West China Center of Excellence for Pancreatitis, Institute of Integrated Traditional Chinese and Western Medicine, Natural and Biomimetic Medicine Research Center, Tissue-Orientated Property of Chinese Medicine Key Laboratory of Sichuan Province, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China.
Introduction: Acute pancreatitis (AP) is a severe inflammatory disease of the pancreas that could trigger a systemic inflammation and multi-organ dysfunction. Stigmasterol, a natural plant sterol found in various herbs and vegetables, exhibits a significant anti-inflammatory, antioxidant, and cholesterol-lowering effects. However, its therapeutic potential in AP have not been thoroughly investigated.
View Article and Find Full Text PDFA human monoclonal antibody isolated from Japanese encephalitis virus vaccine-vaccinated volunteer neutralizing various flaviviruses.
Front Microbiol
December 2024
School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, China.
Introduction: Japanese encephalitis virus (JEV) and Zika virus (ZIKV) are prevalent in over 80 countries or territories worldwide, causing hundreds of thousands of cases annually. But currently there is a lack of specific antiviral agents and effective vaccines.
Methods: In the present study, to identify human neutralizing monoclonal antibody (mAb) against JEV or/and ZIKV, we isolated ZIKV-E protein-binding B cells from the peripheral venous blood of a healthy volunteer who had received the JEV live-attenuated vaccine and performed 10× Genomics transcriptome sequencing and BCR sequencing analysis, we then obtained the V region amino acid sequences of a novel mAb LZY3412.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!