Article
Biochemical Research Methods
Cetin Canpolat, Mehmet Melih Tatlisoz
Summary: In this study, the adsorption of a protein on a nanoparticle with a nanostructured surface was simulated by considering charge regulation. The results showed that factors such as protonation/deprotonation, polarization, topography, and morphology of the surface have an impact on protein adsorption.
Article
Chemistry, Physical
K. P. Greeshma, R. Thamizselvi
Summary: This study reports the synthesis of zinc oxide nanoparticles from combined leaf extracts of Catharanthus roseus and Morinda Citrifolia, and investigates their interaction with cancer protein-synthesizing DNA fragments. Computational analysis and experimental results both demonstrate the potential anticancer properties of these nanoparticles and their potential as drug delivery systems.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemical Research Methods
Cetin Canpolat, Mehmet Melih Tatlisoz
Summary: This study investigates the adsorption mechanism of proteins on charged silica nanoparticles in an aqueous salt medium using an electrical double layer model. The model takes into account polarization, morphology, topography, and protonation/deprotonation effects on the surface chemistry and electrostatic charge within the electrical double layer. Three protein adsorption models (classical Langmuir, extended Langmuir, and two-state) are combined with the charge regulation model to simulate the size- and pH-dependent characteristics of protein adsorption. The effects of various parameters, such as ionic concentration, pH, surface charge density, protein concentration, protein charge, and nanoparticle size, are systematically investigated.
IEEE TRANSACTIONS ON NANOBIOSCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Mattias Sjoberg, Mokhtar Mapar, Antonius Armanious, Vladimir P. Zhdanov, Bjorn Agnarsson, Fredrik Hook
Summary: The label-free evanescent light-scattering microscopy can accurately resolve the binding of proteins to individual lipid vesicles. A theoretical model is proposed to quantify the mass bound to the vesicles based on changes in light-scattering intensity. This method avoids signal interference from nonspecific protein binding and greatly enhances sensitivity through averaging intensities from multiple vesicles.
Article
Chemistry, Applied
Min Huang, Yuling Song, Nan Lv, Chengzhi Liu, Gerui Ren, Qing Shen, Binju Wang, Zexing Cao, Hujun Xie
Summary: The interaction mechanism between zein and lysozyme was investigated in this study. The results showed that zein-lysozyme complex nanoparticles were stable at a ratio of 2:1 and pH 4.0, with electrostatic and hydrophobic interactions being the main driving forces. Hydrogen bonding also played a role, but not as significant. The molecular dynamics simulations revealed that lysozyme preferred to bind to the protruding area of zein, and certain residues in both zein and lysozyme contributed significantly to the binding. These findings provide scientific guidance for the potential application of zein-lysozyme nanoparticles in the food industry as delivery systems or emulsion stabilizers.
FOOD HYDROCOLLOIDS
(2022)
Article
Biochemistry & Molecular Biology
Lingxiao Li, Yuanyuan Yang, Lin Wang, Feng Xu, Yuan Li, Xiaocong He
Summary: As a platform for targeted delivery of imaging and therapeutic agents, nanoparticles have broad applications in cancer diagnosis and treatment. However, the inefficient in vivo delivery of nanoparticles limits their potential for further applications. Upon entering the physiological environment, nanoparticles immediately interact with proteins and form protein corona, which alters their surface properties and affects their transport. This study used molecular dynamics simulations to investigate the adsorption mechanism of nanoparticles with different surface modifications and proteins, as well as their interactions with cell membranes. The results reveal that human serum albumin prefers to interact with hydrophobic and positively charged nanoparticles, while complement protein C3b prefers hydrophobic and charged nanoparticles. Pre-adsorption of human serum albumin on the nanoparticle surface noticeably reduces the interaction between the nanoparticle and C3b. Moreover, a high amount of protein pre-adsorption can decrease the probability of nanoparticle-membrane interaction. These findings suggest that appropriate nanoparticle modification with proteins enhances their targeting capability, which can guide nanoparticle design and improve transport efficiency.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Review
Pharmacology & Pharmacy
Hwankyu Lee
Summary: Molecular dynamics simulations have revealed the impact of protein corona on nanoparticles, showing the competitive adsorption and desorption mechanism of proteins on nanoparticle surfaces, as well as the interactions between protein-coated nanoparticles and cell membranes. These simulations provide insights into the Vroman effect and offer predictions consistent with experimental observations on a molecular scale.
Article
Engineering, Chemical
Wenqian Chen, Thomas N. H. Cheng, Liang Fa Khaw, Xiaoyu Li, Huaiyu Yang, Jinbo Ouyang, Jerry Y. Y. Heng
Summary: Silica nanoparticles can effectively promote lysozyme crystallization, improve crystallization efficiency, and enhance product recovery rate.
SEPARATION AND PURIFICATION TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yuke Xie, Ziqiao Zhong, Wenhao Wang, Ying Huang, Chuanbin Wu, Xin Pan, Zhengwei Huang
Summary: As a widely studied mesoporous silica nanoparticle in drug delivery systems, MCM-41 possesses unique properties but its applications have not been industrialized due to its interaction with biomolecules, especially proteins. This study investigated the interactions between MCM-41 and proteins using BSA, Lyso, and BHb as model proteins. Different interaction patterns were observed, leading to varying effects on protein structure, MCM-41 surface chemistry, and protein adsorption capability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Ting Zhang, Anqi Wu, Xiaosong Hu, Qiyu Deng, Ziyi Ma, Lina Su
Summary: As plant-specific transcription regulators, YABBYs play important roles in plant growth, development and stress responses. This study provides valuable information through phylogenetic analysis, gene structure analysis, protein structure analysis, and gene expression profiling of eight OsYABBYs, indicating their involvement in different developmental processes and functional differentiation. The study also suggests potential interactions between OsYABBYs and WOX proteins, which were confirmed by yeast two-hybrid and luciferase complementation imaging assays. These findings contribute to a better understanding of OsYABBYs regulation mechanism and its potential in improving rice performance.
Review
Biochemistry & Molecular Biology
Yanni Yu, Yaning Luan, Wei Dai
Summary: This review summarizes the recent research on the dynamic process and mechanisms of protein corona formation, which occurs when nanoparticles interact with proteins. The formation of protein corona is a homeostasis process where proteins compete for limited surface sites on nanoparticles. The review also discusses the factors that affect formation and techniques commonly used for protein corona analysis. Furthermore, it assesses the limitations and challenges in protein corona studies and proposes future perspectives.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Leena Hussein Bajrai, Aiah M. Khateb, Maha M. Alawi, Hashim R. Felemban, Anees A. Sindi, Vivek Dhar Dwivedi, Esam Ibraheem Azhar
Summary: This study demonstrates the potential of a diverse set of glycosylated flavonoids as inhibitors of Mtb CYP121. The findings provide a basis for further experimental validation and development of therapies for drug-resistant Mtb strains.
Article
Biochemistry & Molecular Biology
Amanda K. Pearce, Rachel K. O'Reilly
Summary: Significant research efforts have been dedicated to exploring the potential of polymers for biomedical applications in recent decades. The properties of polymers, including chemistry, charge, and self-assembly characteristics, play a crucial role in their interactions with cells and biological membranes. Specifically, the hydrophobicity of polymers has been identified as a key property influencing their efficacy in biomedicine applications.
Review
Biochemistry & Molecular Biology
Turkan Kopac
Summary: Proteins are diverse biopolymers that participate in almost all processes in living cells. When nanoparticles interact with proteins, they form a protein corona layer, which influences their interactions. The characteristics of nanoparticles such as size, surface chemistry, and charge play a critical role in determining the behavior of the protein corona.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Engineering, Environmental
Valentina Bernal, Liliana Giraldo, Juan Carlos Moreno-Pirajan
Summary: This study investigated the interactions between paracetamol and activated carbon, as well as their impact on adsorption capacity. By modifying the physicochemical properties of activated carbon, it was found that an increase in basic groups led to a decrease in relative kinetic constants. The adsorption capacities varied under different solvent conditions, indicating the importance of chemical interactions in the adsorption process.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Biophysics
Abhishek Gupta, Navneet Chandra Verma, Syamantak Khan, Chayan Kanti Nandi
BIOSENSORS & BIOELECTRONICS
(2016)
Article
Chemistry, Multidisciplinary
Abhishek Chaudhary, Syamantak Khan, Abhishek Gupta, Chayan Kanti Nandi
NEW JOURNAL OF CHEMISTRY
(2016)
Article
Chemistry, Analytical
Abhishek Gupta, Navneet Chandra Verma, Syamantak Khan, Shalini Tiwari, Abhishek Chaudhary, Chayan Kanti Nandi
SENSORS AND ACTUATORS B-CHEMICAL
(2016)
Article
Chemistry, Analytical
Navneet C. Verma, Syamantak Khan, Chayan K. Nandi
METHODS AND APPLICATIONS IN FLUORESCENCE
(2016)
Article
Chemistry, Physical
Syamantak Khan, Weixing Li, Narain Karedla, Jan Thiart, Ingo Gregor, Anna M. Chizhik, Joerg Enderlein, Chayan K. Nandi, Alexey I. Chizhik
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2017)
Article
Chemistry, Multidisciplinary
Syamantak Khan, Akshita Sharma, Sourav Ghoshal, Sanjhal Jain, Montu K. Hazra, Chayan K. Nandi
Article
Nanoscience & Nanotechnology
Megan J. Neufeld, Hayden Winter, Madeleine R. Landry, Andrea M. Goforth, Syamantak Khan, Guillem Pratx, Conroy Sun
ACS APPLIED MATERIALS & INTERFACES
(2020)
Article
Oncology
Syamantak Khan, Maxime Bassenne, Jinghui Wang, Rakesh Manjappa, Stavros Melemenidis, Dylan Y. Breitkreutz, Peter G. Maxim, Lei Xing, Billy W. Loo, Guillem Pratx
Summary: The study investigated the effects of ultrahigh-dose-rate radiation (FLASH) on the hypoxic core within tumor spheroids, demonstrating that FLASH irradiation transiently expands the hypoxic core and engulfs well-oxygenated cells, while conventional irradiation steadily replenishes oxygen. This differential response was consistent with computational model predictions, with FLASH irradiation resulting in a dose-modifying factor of around 1.3 for doses above 10 Gy.
INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Syamantak Khan, Sungwoo Kim, Yunzhi Peter Yang, Guillem Pratx
Summary: This study investigated the use of radioluminescence microscopy for imaging FDG uptake in engineered 3D tumor models with high resolution. The method demonstrated the feasibility of separately resolving tumor and stromal components with high spatial resolution, and could potentially be applied to more advanced engineered cancer models as well as surgical tissue slices and tumor biopsies.
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING
(2021)
Article
Multidisciplinary Sciences
Syamantak Khan, June Ho Shin, Valentina Ferri, Ning Cheng, Julia E. Noel, Calvin Kuo, John B. Sunwoo, Guillem Pratx
Summary: A microscopy method has been developed to image organoids using clinical radiotracers, which enables visualization of metabolic activity in patient-derived tumor organoids and potential prediction of therapeutic response. This method shows promise for identifying drug candidates, personalizing treatment regimens, and incorporating clinical imaging biomarkers in organoid-based co-clinical trials.
NATURE COMMUNICATIONS
(2021)
Article
Materials Science, Biomaterials
Yufu Ren, Justin G. Rosch, Madeleine R. Landry, Hayden Winter, Syamantak Khan, Guillem Pratx, Conroy Sun
Summary: The development of radiation responsive materials, such as nanoscintillators, has led to exciting new theranostic applications, particularly in X-ray luminescence computed tomography. A radioluminescent nanoplatform consisting of Tb-doped nanophosphors with a unique core/shell/shell (CSS) architecture has shown bright optical luminescence under X-ray excitation and potential for enhanced DNA damage and cell killing in combination with X-ray irradiation.
BIOMATERIALS SCIENCE
(2021)
Meeting Abstract
Oncology
S. Khan, M. Bassenne, J. Wang, R. Manjappa, B. W. Loo, G. Pratx
INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS
(2020)
Meeting Abstract
Oncology
Syamantak Khan, June Ho Shin, Ning Cheng, Calvin Kuo, John Sunwoo, Guillem Pratx
Article
Nanoscience & Nanotechnology
Syamantak Khan, Navneet C. Verma, Chethana, Chayan K. Nandi
ACS APPLIED NANO MATERIALS
(2018)
Article
Biochemistry & Molecular Biology
Chethana Rao, Syamantak Khan, Navneet C. Verma, Chayan Kanti Nandi