Review
Biochemistry & Molecular Biology
Aaron Morgan, Sarah LeGresley, Christopher Fischer
Summary: The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, and mechanisms such as chromatin remodeling enzymes have evolved to regulate and modify chromatin structure by using the energy from ATP to reposition and rearrange nucleosomes. This review focuses on the nucleosome mobilization activity of these essential molecular machines.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Nousheen Bibi, Ayesha Farid, Sana Gul, Johar Ali, Farhat Amin, Umesh Kalathiya, Ted Hupp
Summary: COVID-19 vaccine will help attenuate the disease progression rates, but its distribution may pose challenges and delays. Repurposed drugs against SARS-CoV-2 could be an attractive strategy, especially in poorly-resourced countries. This study conducted virtual screening of broad-spectrum antiviral agents against key proteins of SARS-CoV-2, identifying drugs with high binding affinities to multiple targets.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Chengwei Zhang, Jing Huang
Summary: The organization of genomes in space and time dimension is crucial for gene expression and regulation. Through explicit-solvent all-atom simulations under physiological conditions, the effective interactions between nucleosomes can be revealed at an atomic level, aiding in the construction of a coarse-grained model for chromatin. Free energy landscapes derived from umbrella sampling simulations are consistent with recent experimental and simulation results, providing valuable insights into the interactions between nucleosomes in solution.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Fritz Nagae, Giovanni B. Brandani, Shoji Takada, Tsuyoshi Terakawa
Summary: Translocases involved in eukaryotic DNA transcription, replication, and repair encounter nucleosomes formed by histone octamers wrapped around genomic DNA, triggering downstream repositioning of nucleosomes. This study identified a lane-switch mechanism for downstream repositioning, where wrapped DNA switches binding lanes after unwrapping, providing insights into transcription through nucleosomes and histone recycling.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biophysics
Ru Zhao, Yingcong Lu, Ce Wang, Xiaoge Zhang, Abbas Khan, Cuina Wang
Summary: This study investigated the binding of curcumin (CUR) with thermally modified beta-lactoglobulin (beta-LG). Different temperature conditions were used to modify beta-LG, and the results showed that pre-heating at 80 degrees C led to the strongest binding affinity. The interaction between CUR and beta-LG80 involved hydrogen bonds and resulted in the transfer of CUR to an amorphous state, while maintaining the antioxidant capacity of both components. Molecular dynamics simulation confirmed the enhanced hydrophobic properties of beta-LG80 compared to native protein.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2023)
Article
Chemistry, Physical
Lim Heo, Collin F. Arbour, Giacomo Janson, Michael Feig
Summary: Protein structures can be determined experimentally or computationally. Computational methods utilize databases for structure prediction, but predicting structures distant from known ones may result in lower accuracy. Physics-based refinement methods can improve model accuracy.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Review
Engineering, Chemical
Yunqiao Ma, Jia Wei Chew
Summary: This review introduces the application of molecular dynamics (MD) simulation in studying membrane fouling and foulant adsorption processes. MD simulations can quantify interfacial physical properties, generate trajectories for adsorption process, and reveal unique characteristics of foulants. The use of enhanced sampling algorithms in biased simulations is also discussed to address the limitations of unbiased simulations and quantify the free energy landscape. Future perspectives on enhancing the value of MD as a tool for understanding and predicting membrane fouling are proposed.
JOURNAL OF MEMBRANE SCIENCE
(2022)
Article
Chemistry, Physical
Umberto Raucci, Valerio Rizzi, Michele Parrinello
Summary: This article proposes a modular workflow for blind reaction discovery and determination of reaction paths. The workflow utilizes advanced sampling methods and neural network-based collective variables to improve sampling and refinement of results. The approach can extend the power of ab initio molecular dynamics in exploring and characterizing reaction space.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Christopher Faulkner, Nora H. de Leeuw
Summary: Fentanyl, a potent opioid analgesic, is used in combination with propofol in general anesthesia. Molecular dynamics simulations revealed that fentanyl acts as a stabilizer, helping propofol to remain in binding sites. This study provides insights into the interactions between different drugs in the anesthesia process.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Pawan Kumar, Deepak Sheokand, Annu Grewal, Vandana Saini, Ajit Kumar
Summary: This study used a drug repositioning strategy to identify potential anti-epileptic drugs by evaluating the clinical side effect similarities of drugs in a database. Paroxetine showed better binding affinities to target receptors and has potential as a candidate for epilepsy treatment.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Multidisciplinary
Zhiyang Zhang, Jianwu Lv, Yu Wang, Hongli Yu, Baolin Guo, Jihang Zhai, Chaojie Wang, Yuan Zhao, Fangfang Fan, Wen Luo
Summary: This study improves the residence time of galantamine, a drug used for symptomatic treatment of Alzheimer's disease, by modifying the inhibitor of Acetylcholinesterase (AChE). The researchers found that galantamine simply occupies a catalytic anionic site and its release from AChE requires only about 8.6 kcal/mol of energy. Through computational approaches and experimental combinations, novel galantamine derivatives with longer residence time were designed.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Review
Chemistry, Applied
Xingran Kou, Dongdong Su, Fei Pan, Xiwei Xu, Qingran Meng, Qinfei Ke
Summary: This review provides a systematic discussion of the application of molecular dynamics (MD) simulations in aroma compounds (ACs)/cyclodextrins (CDs) inclusion complexes (ICs). It covers the establishment of the simulation process, parameter selection, model evaluation, and various application cases, summarizing the major achievements and challenges of this method.
CARBOHYDRATE POLYMERS
(2024)
Article
Biochemistry & Molecular Biology
Ye Ding, Kuang Yu, Jing Huang
Summary: Recent advances in data science have influenced the development of classical force fields. This review examines the use of data science techniques such as database construction, atom typing, and machine learning potentials in force field development. It highlights the effectiveness of new tools like active learning and automatic differentiation in generating target data and fitting with macroscopic observables. The article also discusses philosophical changes in the construction and usage of force field models. It emphasizes the potential for developing more accurate biomolecular force fields using data science techniques.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Review
Construction & Building Technology
Salim Barbhuiya, Bibhuti Bhusan Das
Summary: This paper presents a comprehensive review of the application of molecular dynamics simulation in concrete research. The study provides an overview of the principles, applications, and types of molecular dynamics simulation, focusing on its role in enhancing the understanding of concrete properties. It critically examines existing research studies, explores simulation techniques and future directions, and discusses the potential impact of this approach on the sustainability of the construction industry.
JOURNAL OF BUILDING ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Caitlin M. MacCarthy, Jan Huertas, Claudia Ortmeier, Hermann vom Bruch, Daisylyn Senna Tana, Deike Reinke, Astrid Sander, Tim Bergbrede, Ralf Jauch, Hans R. Schoeler, Vlad Cojocaru
Summary: Through experiments and molecular simulations, this study reveals how the pioneer factor Oct4 interprets and enhances nucleosome structural flexibility. Oct4 uses its DNA binding domains to propagate and stabilize open nucleosome conformations, providing a structural basis for the versatility of transcription factors' interaction with nucleosomes.
NUCLEIC ACIDS RESEARCH
(2022)