Editorial Material
Multidisciplinary Sciences
J. Pedro de Souza, Howard A. Stone
Summary: Protein condensation can not only form membraneless organelles, but also regulate the availability of water.
Article
Multidisciplinary Sciences
Hugo Wioland, Antoine Jegou, Guillaume Romet-Lemonne
Summary: This article summarizes the experimental method of using optical microscopy to observe individual events on individual actin filaments in real time, and discusses its application in understanding actin assembly dynamics. The article also proposes a set of guidelines in order to better utilize this experimental tool.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Multidisciplinary Sciences
Marina. G. G. Guenza
Summary: Many biological processes rely on protein aggregates that have dynamic behaviors spanning different scales. A clever combination of spectroscopy and simulation can be used to investigate these diverse dynamics.
Review
Biochemistry & Molecular Biology
Marco Giulini, Marta Rigoli, Giovanni Mattiotti, Roberto Menichetti, Thomas Tarenzi, Raffaele Fiorentini, Raffaello Potestio
Summary: The increasing computer power and improved accuracy of atomistic force fields have enabled researchers to study biological systems at the molecular level in detail. However, the length and time scales of many processes of interest are still out of reach for current hardware, leading to important questions remaining unanswered. Coarse-grained models, simplified representations of molecules at a lower resolution than atomistic, are commonly used in the investigation of biological physics problems, but the optimal degree of simplification remains a crucial open issue.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biology
Maurizio Brunori
Summary: This article is an extensive report on Italian science, highlighting the challenges faced by Italian scientists within the political system. It reveals the insufficient support for fundamental research in Italy. The report also mentions the ranking of four top Italian scientists and the tradition of Eraldo Antonini Lectures.
Article
Biochemistry & Molecular Biology
Atip Lawanprasert, Janna N. Sloand, Mariangely Gonzalez Vargas, Harminder Singh, Tomer Eldor, Michael A. Miller, Sopida Pimcharoen, Jian Wang, Scott M. Leighow, Justin R. Pritchard, Nikolay V. Dokholyan, Scott H. Medina
Summary: Fluorine has become important in protein design, altering their folding, stability, oligomerization, and bioactivity. Perfluorinated amphiphiles can noncovalently modify proteins, changing their conformation and facilitating their dispersion in fluorous phases. Through various approaches, we establish structure-activity relationships and explore their impact on protein dynamics and intracellular trafficking. This research could contribute to the rational design of fluorinated proteins, inform on potential toxicity of perfluoroalkyl substances, and aid in the development of fluorine-modified biologics for drug discovery and delivery applications.
Article
Biology
Shimaa A. Abdellatef, Hisashi Tadakuma, Kangmin Yan, Takashi Fujiwara, Kodai Fukumoto, Yuichi Kondo, Hiroko Takazaki, Rofia Boudria, Takuo Yasunaga, Hideo Higuchi, Keiko Hirose, Andrew P. Carter
Summary: The bending of cilia and flagella is caused by the oscillatory movement of dynein molecules. Researchers constructed a simple model system to study the oscillation of dynein and found that it can cause repetitive bending motions even without additional regulatory structures.
Editorial Material
Multidisciplinary Sciences
Debora S. Marks, Stephen W. Michnick
Summary: An integrated technique is introduced to quantify and disentangle the effects of gene mutations on protein traits, allowing assessments of mutational effects on protein biophysics.
Article
Biochemistry & Molecular Biology
Melina Daniilidis, Matthias J. Brandl, Franz Hagn
Summary: Membrane mimetics play a crucial role in studying the structure and function of membrane proteins. In this study, the authors compared the biophysical properties of circularized and linear nanodiscs and found that circularized nanodiscs have improved membrane fluidity and size stability, making them advantageous for high-resolution NMR studies at elevated temperatures.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Genetics & Heredity
Nikhil Mishra, Carl-Philipp Heisenberg
Summary: The development of complex shapes in multicellular organisms from single-celled zygotes, known as morphogenesis, involves an interplay between genetic, cellular, and mechanical factors. Multidisciplinary approaches at the interface of biology, physics, and mathematics have historically been used to study morphogenesis. Recent technological advances have improved our ability to visualize, analyze, and manipulate the genetic and biophysical factors involved in morphogenesis.
ANNUAL REVIEW OF GENETICS, VOL 55
(2021)
Article
Biochemistry & Molecular Biology
Carter J. Wilson, Wing-Yiu Choy, Mikko Karttunen
Summary: The development of AlphaFold2 has brought a paradigm shift in structural biology and has shown excellent performance in predicting disordered regions. The accuracy of the constructed disorder predictor from AlphaFold2 structures varies, with the naive assumption of assigning residues to ordered or disordered based on helices, strands, and H-bond stabilized turns leading to a significant overestimation of disorder. The predicted local distance difference test (pLDDT) provides a reliable measure of residue-wise disorder and shows an interesting relationship with secondary structure.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Maria A. Toscanini, Alvaro A. Recoulat Angelini, Maria F. Troncoso, Lucrecia M. Curto
Summary: The use of iMolview Lite in the activity helps students understand the relationship between protein structure and function, receiving positive feedback from students as a friendly and engaging learning method.
JOURNAL OF CHEMICAL EDUCATION
(2021)
Article
Chemistry, Multidisciplinary
Elke De Zitter, Siewert Hugelier, Sam Duwe, Wim Vandenberg, Alison G. Tebo, Luc Van Meervelt, Peter Dedecker
Summary: Anisotropic environments can significantly impact the spectroscopy and photochemistry of molecules, leading to complex structure-function relationships. By studying fluorescent proteins as model systems, it was found that changes in spectroscopic properties can be attributed to multiple underlying mechanisms. The research highlights the complex interplay between structure and spectroscopy, identifying key modulators like polarity, hydrogen bonding, and presence of water molecules.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Gabriel Ortega, Miguel A. Aguilar, Bishal K. Gautam, Kevin W. Plaxco
Summary: The interactions of proteins with surfaces play a crucial role in biological processes and biotechnologies, with electrostatics being a key factor. The content of charged amino acids in proteins determines the extent of stabilization by surfaces.
Article
Chemistry, Physical
Milan Kumar Hazra, Yaakov Levy
Summary: In this study, the effects of short-range interactions and long-range electrostatic interactions on the stability, structure, and dynamics of liquid-liquid phase separation in protein condensates were investigated using coarse-grained molecular dynamics simulations. It was found that an increase in short-range interactions at the expense of long-range electrostatic interactions led to a decrease in critical temperature of phase separation. Additionally, sequences with a high fraction of short-range interactions exhibited some stabilization, compensating for the loss of long-range interactions. Furthermore, the exchange of long-range electrostatic interactions for short-range interactions impacted the kinetics of breaking intermolecular contacts and intramolecular fluctuations, ultimately affecting the liquid-like behavior of protein condensates.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biophysics
Roja Hadianamrei, Mhd Anas Tomeh, Stephen Brown, Jiqian Wang, Xiubo Zhao
Summary: This study focused on the development and characterization of short cationic amphiphilic beta-sheet forming anticancer peptides. The peptides exhibited selective anticancer activity influenced by their surface activity and secondary structure in hydrophobic surfaces, leading to disruption of mitochondrial membranes and apoptosis. Insights gained from the study can be used to design new ACPs with improved anticancer activity and lower toxicity against normal cells.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2022)
Article
Chemistry, Physical
Roja Hadianamrei, Mhd Anas Tomeh, Stephen Brown, Jiqian Wang, Xiubo Zhao
Summary: The study introduced a new library of short cationic amphiphilic α-helical anticancer peptides with selective cytotoxicity against colorectal and cervical cancer, and investigated their anticancer mechanisms through a series of experiments.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Materials Science, Biomaterials
Ting Dai, Jiayi Ma, Su Ni, Chun Liu, Yan Wang, Siyu Wu, Jun Liu, Yiping Weng, Dong Zhou, Ana Jimenez-Franco, Hongbin Zhao, Xiubo Zhao
Summary: Electrospun PCL scaffolds, widely used in tissue engineering, have the potential to mimic the natural extracellular matrix structure. However, their small pore size and low bioactivity hinder cell migration and tissue formation. In this study, different materials were used to fabricate porous scaffolds, and the removal of water-soluble fibers increased the porosity. Biocompatibility and osteogenesis were evaluated, and the results showed that washed PCL/PEG/ATP scaffolds promoted better cell infiltration and differentiation into osteoblasts compared to PCL scaffolds. In vivo studies also demonstrated enhanced bone regeneration in rat cranium defects using ATP-doped electrospun PCL scaffolds.
BIOMATERIALS ADVANCES
(2022)
Article
Pharmacology & Pharmacy
Ruicheng Xu, Mhd Anas Tomeh, Siyuan Ye, Peng Zhang, Songwei Lv, Rongrong You, Nan Wang, Xiubo Zhao
Summary: The study demonstrated the use of microfluidic swirl mixers for large-scale production of liposomes with high productivity and better size control. These liposomes effectively delivered curcumin into cancer cells, showing promising potential for drug delivery systems.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2022)
Article
Engineering, Biomedical
Wen Qin, Chenkai Li, Chun Liu, Siyu Wu, Jun Liu, Jiayi Ma, Wenyang Chen, Hongbin Zhao, Xiubo Zhao
Summary: In this study, 3D printed GO/ATP/COL composite scaffolds were developed. The composite scaffolds showed excellent printability and mechanical strength. In vitro and in vivo experiments demonstrated that the composite scaffolds exhibited good biocompatibility and osteogenic ability, promoting bone tissue regeneration.
JOURNAL OF BIOMATERIALS APPLICATIONS
(2022)
Article
Chemistry, Analytical
Songwei Lv, Dong Zheng, Zhaoxian Chen, Bin Jia, Peng Zhang, Jiaxuan Yan, Xiubo Zhao, Wanlan Jiang, Jing-Juan Xu
Summary: This study designed a near-infrared light-responsive microfluidic chip for biocompatible single-cell manipulation and study of CTC heterogeneity. The chip combined immunomagnetic labeling and a gradient magnetic field to distribute CTCs in different regions. The lateral flow microarray chip achieved high capture efficiency and purity, and the captured single CTC cell can be released individually by near-infrared at a specific point.
ANALYTICAL CHEMISTRY
(2023)
Article
Biophysics
Xinyu Xu, Yujie Ding, Roja Hadianamrei, Songwei Lv, Rongrong You, Fang Pan, Peng Zhang, Nan Wang, Xiubo Zhao
Summary: This study demonstrates the potential application of functionalized gold nanorods with antimicrobial peptides in photothermal therapy for bacterial infections. The conjugation of peptides increased selectivity, antimicrobial activity, and biocompatibility of the gold nanorods. The experiments conducted in vitro and in a mouse model of wound infection highlight the effective antimicrobial effects and wound healing properties of the peptide-functionalized gold nanorods with and without laser irradiation.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2022)
Article
Chemistry, Multidisciplinary
Yi Jin, Mhd Anas Tomeh, Peng Zhang, Mingzhu Su, Xiubo Zhao, Zhiqiang Cai
Summary: This study utilized a newly developed microfluidic swirl mixer to fabricate temperature-sensitive liposomes (TSL) for the treatment of breast cancer through near-infrared stimulation. The results demonstrated that AP-3/ICG@TSL significantly inhibited the growth of breast cancer both in vitro and in vivo without causing damage to other organs. These findings suggest that the AP-3/ICG@TSL manufactured using the microfluidic swirl mixer is a promising drug delivery system for breast cancer therapy.
Review
Materials Science, Multidisciplinary
Nan Wang, Xiubo Zhao
Summary: This article systematically introduces the important role of atomic force microscopy (AFM) in studying contact electrification (CE) phenomena, especially in researching the CE mechanism at the nanoscale. In addition, the working mechanism of metal-semiconductor direct current triboelectric nanogenerators based on conductive atomic force microscopy (C-AFM) studies is also introduced. The potential utility and limitations of AFM in future TENG technology development and its improvement direction are analyzed. This review provides an updated overview and understanding of the existing challenges and opportunities, and it is hoped to contribute to the advancement of TENG technologies.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Article
Biochemistry & Molecular Biology
Roja Hadianamrei, Mhd Anas Tomeh, Jiqian Wang, Stephen Brown, Xiubo Zhao
Summary: In this study, two new surfactant-like peptides (SLPs), named (IA)4K and (IG)4K, were developed for selective delivery of antisense oligodeoxynucleotides (ODNs) and small interfering RNA (siRNA) to cancer cells. The interaction of the peptides with nucleic acids, their transfection efficiency, and cytotoxicity were investigated. Both SLPs showed high transfection efficiency and selectivity for cancer cells, and exhibited low cytotoxicity. This study provides insights into the structural features required for nucleic acid complexation and delivery, and serves as a guide for the design of new SLPs for selective gene delivery to minimize adverse effects in healthy tissues.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Materials Science, Biomaterials
Yu Xia, Ruicheng Xu, Siyuan Ye, Jiaxuan Yan, Piyush Kumar, Peng Zhang, Xiubo Zhao
Summary: Current anticancer research suggests that combining multiple treatment methods can enhance the killing of tumor cells. In this study, we developed multi-responsive targeted antitumor nanoparticles (NPs) using microfluidic swirl mixer technology. The NPs were made of folate-functionalized gelatin NPs, CuS NPs, Fe3O4 NPs, and curcumin. The results showed that the combination of photothermal-ablation therapy, chemotherapy, and targeted delivery of the NPs efficiently killed tumor cells.
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2023)
Article
Biophysics
Piyush Kumar, Ana Jimenez Franco, Xiubo Zhao
Summary: 3D cell culture is a technique that mimics in vivo environment for cells to grow in vitro. This study proposes two independent 3D cell culture models for different applications. One uses porous spherical structures as carriers to retain cell shape, while the other uses 3D printed silk fibroin structures for directed cell growth. These models have advantages in cell research, such as drug discovery and treatment of neuropathies.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2023)
Article
Chemistry, Physical
Jinguo Qiu, Mhd Anas Tomeh, Yi Jin, Bo Zhang, Xiubo Zhao
Summary: This study presented a high-performance microfluidic device to fabricate ACP loaded nanoparticles (NPs) with controllable properties. The encapsulated ACP showed reduced toxicity, controlled release, and increased cell uptake, leading to enhanced anticancer effects. The development of At3 loaded NPs provides a promising approach for ACP-based cancer therapy.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Materials Science, Biomaterials
Songwei Lv, Jingfang Wang, Rongrong You, Suyu Liu, Yujie Ding, Roja Hadianamrei, Mhd Anas Tomeh, Fang Pan, Zhiqiang Cai, Xiubo Zhao
Summary: This study investigated the relationship between the chemical structure and biological activity of AMPs derived from a naturally occurring AMP from ants. The designed peptides showed enhanced antibacterial activity by replacing cationic amino acids with hydrophobic amino acids in the hydrophobic region, and improved selectivity for bacteria by increasing the number of cationic amino acids in the hydrophilic region. Four of the designed peptides displayed significant antibacterial activity and high selectivity for bacteria. The results can provide a better understanding of the structural features required for strong antibacterial activity and selectivity, and guide the future rational design of AMPs.
BIOMATERIALS SCIENCE
(2022)
Article
Materials Science, Biomaterials
Jiayi Ma, Siyu Wu, Jun Liu, Chun Liu, Su Ni, Ting Dai, Xiaoyu Wu, Zhenyu Zhang, Jixin Qu, Hongbin Zhao, Dong Zhou, Xiubo Zhao
Summary: Hydroxyapatite (HA) has limitations in bone defect treatment due to the lack of angiogenic properties and undesirable mechanical properties. This study utilized nanoattapulgite (ATP) to enhance the bioactivity of HA scaffolds for bone regeneration. The incorporation of ATP improved the printing fidelity and mechanical properties of the scaffolds in vitro, and increased the expression levels of osteogenic and vascularization-related genes. In vivo experiments demonstrated that the PVA/COL/ATP/HA scaffolds promoted vascularization and bone formation in a rabbit tibial defect model. The combination of ATP and HA shows promise for vascularized bone tissue engineering.
BIOMATERIALS SCIENCE
(2022)
