Article
Biochemistry & Molecular Biology
Vladimir Vanik, Zuzana Bednarikova, Gabriela Fabriciova, Steven S. -S. Wang, Zuzana Gazova, Diana Fedunova
Summary: Amyloid fibrils can be modulated by ionic liquids, and the speed and morphology of fibrillization depend on the concentration and type of ions. The presence of different ions in ionic liquids can promote or hinder the formation of amyloid fibrils. The specific protein-ion interactions and long-range electrostatic shielding play important roles in the impact of ionic liquids.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Mantas Ziaunys, Kamile Mikalauskaite, Andrius Sakalauskas, Vytautas Smirnovas
Summary: The fluctuation in solution ionic strength has a significant impact on the inhibitory effect of the protein aggregation inhibitor, epigallocatechin-3-gallate, with different amyloid-forming proteins exhibiting unique responses.
Article
Polymer Science
Shuang Wei, Zechuan Zhang, Weibin Dong, Ting Liang, Junyi Ji, Wen Tian, Shuai Tan, Qiang Zhao, Caihong Wang, Yong Wu
Summary: Ionic species play an important role in the phase separation behavior of PNIPAm in aqueous solutions, with different ions having varying effects on clouding temperatures. Particularly, the structure of azobenzene molecules under visible light irradiation affects the temperature response of PNIPAm.
MACROMOLECULAR RAPID COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Chi-Chang Wu, Min-Rong Wang
Summary: A single-crystalline silicon nanobelt field-effect transistor (SiNB FET) device was developed for pH and biomolecule sensing, with buffer concentration shown to affect sensitivity and stability. The sensor demonstrated sensitivity to solution pH and AFP, with results indicating a negative relationship between buffer concentration and sensor sensitivity. Surface functionalization was found to impact AFP sensing effectiveness, with buffer concentration influencing current shifts in the sensor. Overall, buffer concentration plays a crucial role in the sensitivity and stability of the SiNB FET device in chemical and biomolecular sensing.
Article
Chemistry, Physical
Thomas Bourke, Kasimir P. Gregory, Alister J. Page
Summary: The origins and behaviour of specific ion effects have been extensively studied in water and nonaqueous molecular solvents. However, the impacts of specific ion effects on more complex solvents, such as nanostructured ionic liquids, are still unclear. This study hypothesizes that the influence of dissolved ions on the hydrogen bonding in nanostructured ionic liquid PAN constitutes a specific ion effect.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Mantas Ziaunys, Andrius Sakalauskas, Kamile Mikalauskaite, Vytautas Smirnovas
Summary: Researchers conducted extensive studies on the aggregation reactions of alpha-synuclein and found that both ionic strength and protein concentration are crucial factors determining the structural variability of alpha-synuclein amyloid fibrils. Their study shows that even under identical conditions, up to four distinct types of aggregates can be observed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Engineering, Chemical
Navpreet Singh, Paras H. Gopani, Hemanta K. Sarma, Padmaja Mattey, Digambar S. Negi, Vivek R. Srivastava, Thomas Luxbacher
Summary: The study aims to indirectly estimate the zeta potential for high salinity brine using measurements for low salinity brine and develop an understanding of electrostatic shielding as predicted by the electric double layer (EDL) model.
CANADIAN JOURNAL OF CHEMICAL ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Wayne Travers, Fintan Kelleher
Summary: Nisin is an effective lantibiotic with activity against Gram-positive bacteria and food-borne pathogens. The study found that salts, including NaCl, can affect the activity and stability of nisin under different conditions.
BIOPHYSICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Xiupeng Chen, Xian Kong
Summary: Solid polymer electrolytes (SPEs) with low ionic conductivity are potential materials for next-generation lithium metal batteries. Nanostructured materials can provide better performance for SPEs. Molecular dynamics simulation is used to investigate SPEs under nanoscale confinement, which has shown to accelerate the transport of neutral molecules. The results reveal that ion diffusion accelerates significantly while the ionic conductivity does not increase significantly in parallel due to enhanced ion association with decreasing channel size.
Article
Chemistry, Analytical
Lina Diao, Zhan Xu, Wangyang Zhang, Bin Miao, Yimin Hu, Zhiqi Gu, Jiadong Li
Summary: In this study, a simple APTES/PEG-AlGaN/GaN HEMT biosensor was proposed for direct detection in high ionic strength solutions. The PEG modification on the GaN surface established a stable screening system to overcome Debye shielding. The experimental results showed that the APTES/PEG modification strategy enabled direct detection of biomolecules in physiological solutions, providing a new method for bio-surface modification on GaN and advancing the practical application of AlGaN/GaN HEMT biosensors.
Article
Polymer Science
Julija Reitenbach, Christina Geiger, Peixi Wang, Apostolos Vagias, Robert Cubitt, Dirk Schanzenbach, Andre Laschewsky, Christine M. Papadakis, Peter Mueller-Buschbaum
Summary: The swelling behavior of PNIPMAM thin films containing magnesium salts in water vapor is investigated for their potential applications as nanodevices. In situ time-of-flight neutron reflectometry is used to probe the extent and kinetics of the swelling ratio and water content. In situ Fourier-transform infrared (FTIR) spectroscopy and two-dimensional FTIR correlation analysis are utilized to study the solvation events and enhance the sensitivity of PNIPMAM thin films. The addition of Mg(ClO4)2 or Mg(NO3)2 results in higher water uptake and thickness gain in the swollen state, with Mg(NO3)2 showing the highest relative water uptake.
Article
Biochemistry & Molecular Biology
Lucie Khemtemourian, Federico Antoniciello, Bikash R. Sahoo, Marion Decossas, Sophie Lecomte, Ayyalusamy Ramamoorthy
Summary: Human islet amyloid polypeptide (hIAPP) is a key peptide involved in the progression of type-2 diabetes (T2D), forming amyloid fibrils under certain conditions. The sequence variation of IAPP among species strongly influences its amyloidogenicity and toxicity, with residue histidine at position 18 playing a crucial role. Insulin and zinc are natural stabilizing agents that may prevent hIAPP fibril formation, with residue-18 mediating the interactions and zinc binding possibly occurring in the N-terminal region of hIAPP.
CHEMISTRY AND PHYSICS OF LIPIDS
(2021)
Article
Chemistry, Physical
Feng Li, Xenia V. Medvedeva, Jury J. Medvedev, Evgeniia Khairullina, Helen Engelhardt, Skandan Chandrasekar, Yinzhou Guo, Jian Jin, Anna Lee, Heloise Therien-Aubin, Aftab Ahmed, Yuanjie Pang, Anna Klinkova
Summary: The study investigates how electrochemical and complex current behaviors influence the structural stability of nanoscale objects during electrocatalysis.
Article
Chemistry, Physical
Athena E. Metaxas, Vishal Panwar, Ruth L. Olson, Cari S. Dutcher
Summary: The study shows that increasing ionic strength in solution leads to a decrease in floc size, but the growth rate of flocs initially increases then decreases. Higher ionic strength results in denser bentonite aggregates that are more resistant to shear-induced breakage, but may reduce the ability of the polyelectrolyte to bridge multiple bentonite aggregates.
Article
Chemistry, Physical
Pooja Meena, Nand Kishore
Summary: The study reveals the significant role of ionic strength in influencing the interactions between amino acids and sorbitol + NaCl in aqueous solutions. Moreover, sorbitol has been shown to reduce the deleterious effect of salt on protein stability. The association between sodium chloride ions and sorbitol alters the water-mediated effects.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Biochemistry & Molecular Biology
Daeun Noh, Rebekah L. Bower, Debbie L. Hay, Alexander Zhyvoloup, Daniel P. Raleigh
ACS CHEMICAL BIOLOGY
(2020)
Article
Chemistry, Physical
Junjie Zou, Shifeng Xiao, Carlos Simmerling, Daniel P. Raleigh
Summary: Proteins fold on smooth free energy landscapes biased toward the native state, but even rapidly folding proteins can experience roughness on their landscapes. The interactions in the denatured state ensemble under native conditions are challenging to quantify, and non-native interactions can stabilize native backbone structure in the ensemble. Computational and experimental approaches can provide insight into these interactions that cannot be obtained with either method alone.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemistry & Molecular Biology
Karl Kochanowski, Hiroyuki Okano, Vadim Patsalo, James Williamson, Uwe Sauer, Terence Hwa
Summary: This study identifies the regulatory mechanisms that coordinate catabolism and anabolism in Escherichia coli, showing that a simple global gene regulatory program mainly implemented by the transcription factor Crp plays a crucial role in allocating proteomic resources and adjusting metabolic fluxes. In addition, passive changes in local metabolite concentrations contribute to the robust coordination of individual metabolic reactions.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Albert L. Mueller, Wenyu Gu, Vadim Patsalo, Jorg S. Deutzmann, James R. Williamson, Alfred M. Spormann
Summary: The study systematically characterized the physiology of Methanococcus maripaludis during slow growth under energy-limiting conditions, revealing a different resource allocation strategy compared to commonly studied versatile chemoheterotrophic bacteria. Despite slow growth, the methanogenic archaeon maintained its maximum methanogenesis capacity over a wide range of growth rates, with adjustments in energy usage and maintenance energy per biomass.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Ming-Hao Li, Lakshan Manathunga, Erwin London, Daniel P. Raleigh
Summary: The fluorescent dye DPH interacts with amyloid fibrils formed by h-amylin, resulting in increased fluorescence. The time course of amyloid formation can be monitored using DPH, and it may be useful for studying mutant amyloids.
Article
Chemistry, Physical
Junjie Zou, Zhipeng Li, Shuai Liu, Chunwang Peng, Dong Fang, Xiao Wan, Zhixiong Lin, Tai-Sung Lee, Daniel P. Raleigh, Mingjun Yang, Carlos Simmerling
Summary: In drug discovery, altering drug compound structures to improve binding affinity and properties is common. This study presents a new method for simulating the challenging process of "scaffold hopping", demonstrating high accuracy in modeling linker contraction or expansion.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Multidisciplinary
Ming-Hao Li, Daniel P. Raleigh, Erwin London
Summary: The natural asymmetry of cellular membranes affects their properties. Methods involving cyclodextrin have been developed for preparing asymmetric vesicles, enhancing their resistance to leakage and improving stability.
Correction
Biochemistry & Molecular Biology
Ming-Hao Li, Lakshan Manathunga, Erwin London, Daniel P. Raleigh
Article
Microbiology
Ravi Chawla, Steven Klupt, Vadim Patsalo, James R. Williamson, Lisa R. Racki
Summary: The protein AlgP is found to be associated with polyP granules and is required for their even spacing. AlgP binds to the chromosome and inhibits fusion between polyP granules, resulting in their evenly spaced distribution. This discovery provides insights into the functional significance of granule organization during starvation.
Article
Endocrinology & Metabolism
Joseph J. Castillo, Alfred C. Aplin, Daryl J. Hackney, Meghan F. Hogan, Nathalie Esser, Andrew T. Templin, Rehana Akter, Steven E. Kahn, Daniel P. Raleigh, Sakeneh Zraika, Rebecca L. Hull
Summary: The study found that aggregation of IAPP is toxic to islet endothelial cells and induces inflammatory responses, resulting in decreased capillary density, increased capillary diameter, and an increased number of pericytes.
Article
Biochemistry & Molecular Biology
Lakshan Manathunga, Alexander Zhyvoloup, Aria Baghai, Daniel P. Raleigh
Summary: Islet amyloid polypeptide (IAPP) is a 37-residue polypeptide hormone secreted by pancreatic β-cells. It plays a role in glycemic regulation, but in the pre-type-2 diabetic state, it forms amyloid aggregates that contribute to β-cell dysfunction and disease progression. This study investigates the role of aromatic residues in modulating the time course of amyloid formation and cytotoxicity. The results reveal that F23 plays a dominant role and has both accelerating and slowing effects on amyloid formation, as well as influences toxicity.
Article
Biochemistry & Molecular Biology
Matthew E. T. Miller, Ming-Hao Li, Aria Baghai, Vincent H. Peetz, Alexander Zhyvoloup, Daniel P. Raleigh
Summary: Human islet amyloid polypeptide (hIAPP) plays a significant role in the development of diabetes and beta-cell dysfunction. Sheep and goat IAPP have low amyloid formation and toxicity compared to hIAPP. Studying IAPP from different species can provide insights for designing soluble analogues of the human peptide.
Article
Chemistry, Analytical
Konstantinos Thalassinos, Charles Eldrid, Tristan Cragnolini, Aisha Ben-Younis, Junjie Zou, Daniel P. . Raleigh
Summary: Native mass spectrometry combined with ion mobility and collisional activation is an important method for studying protein unfolding. By using unbiased molecular dynamics simulations, the in vacuo unfolding behavior of a well-studied protein, N-terminal domain of ribosomal L9, was found to replicate the behavior observed in solution. However, the theoretical collision cross section of the simulations was slightly lower than that of the experimental data, possibly due to reduced sampling.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Lakshan Manathunga, Rehana Akter, Alexander Zhyvoloup, Carlos Simmerling, Daniel P. P. Raleigh
Summary: Amyloids are protein deposits implicated in various diseases. Disrupting the tight packing in amyloid fibrils affects their formation kinetics. Substitutions with larger amino acids disrupt packing and destabilize fibril structures, while specific substitutions can enhance or slow down amyloid formation.
Article
Biochemical Research Methods
Henry M. Sanders, Farzaneh Chalyavi, Caitlyn R. Fields, Marius M. Kostelic, Ming-Hao Li, Daniel P. Raleigh, Martin T. Zanni, Michael T. Marty
Summary: The aggregation of islet amyloid polypeptide (IAPP) is associated with beta-cell dysfunction in type 2 diabetes (T2D) in humans. The interaction of IAPP oligomers with lipid membranes can disrupt the bilayer integrity and/or homeostasis of the cell. Amino acid sequence variations of IAPPs between species can greatly decrease their propensity for aggregation.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)