Article
Chemistry, Physical
Ying Yuan, Zhonghua Ma, Feng Wang
Summary: A new force field AFM2020 has been developed using the adaptive force matching method for simulating hydrated alanine polypeptides, showing better accuracy compared to other models. The force field predicts different conformations for Ala(7), with a higher helical population than previous estimates based on the same experimental data. Gas-phase simulations suggest that the force field developed from AFM solution-phase data may produce a reasonable conformation distribution in the absence of hydration water, such as the interior of a protein.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Applied
Xinyue Yan, Yijia Jia, Hui Man, Shiyan Sun, Yuyang Huang, Baokun Qi, Yang Li
Summary: Tracking the dynamic changes in kidney bean protein isolate (KPI) structure during extreme pH-shifting reveals mechanisms driving unfolding and refolding from a conformational perspective and its relationship with function. Acidic-shifting affects hydrophobic interactions, while alkaline-shifting affects hydrogen bonding and electrostatic interactions. pH-shifting transforms KPI into spherical and rod-like structures, improving its physical and functional properties. pH-shifting treatment expands the application scope of KPI in the food industry.
Article
Polymer Science
Zahn Stanvliet, Yiyi Deng, Dietmar Appelhans, Silvia Moreno, Susanne Boye, Jens Gaitzsch, Albena Lederer
Summary: This study investigates the temperature sensitivity of polymeric nanoparticles based on tertiary amine methacrylate block copolymers. The research shows that these nanoparticles can undergo a reversible morphological transformation in response to changes in pH and temperature. The findings also demonstrate the ability to lock their intermediate self-assembly structures through cross-linking and validate the morphology transition using analytical tools, which opens up new possibilities for responsive nanocarriers.
Article
Biophysics
Yan Li, Luuk K. Koopal, Yanjun Chai, Wenfeng Tan, Chunyan Wu, Xu Tang, Yi Chen
Summary: Urease in soil interacts with humic acid, resulting in changes in its enzymatic activity and stability. This study investigated the structural changes of urease in the presence of humic acid and the microenvironments of specific residues using spectroscopic techniques. The results showed that humic acid inhibited the fluorescence intensity of urease, but had little effect on the microenvironments of the specific residues. The interaction between urease and humic acid was found to be pH-dependent. The findings provide a better understanding of the behavior of negatively charged proteins in natural environments.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2022)
Article
Engineering, Geological
Shuai Qu, Jianjin Yang, Yang Feng, Yeye Peng, Chunfa Zhao, Shengyang Zhu, Wanming Zhai
Summary: This paper investigates the vibration induced by medium-low speed maglev trains through numerical study and proposes a hybrid prediction model. The research reveals the transmission behavior of maglev train-induced vibration in layered soils and possible causes of vibration amplification phenomena, providing insights for understanding the impact of daily maglev trains on the neighboring environment.
SOIL DYNAMICS AND EARTHQUAKE ENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Lea El Khoury, Zhifeng Jing, Alberto Cuzzolin, Alessandro Deplano, Daniele Loco, Boris Sattarov, Florent Hedin, Sebastian Wendeborn, Chris Ho, Dina El Ahdab, Theo Jaffrelot Inizan, Mattia Sturlese, Alice Sosic, Martina Volpiana, Angela Lugato, Marco Barone, Barbara Gatto, Maria Ludovica Macchia, Massimo Bellanda, Roberto Battistutta, Cristiano Salata, Ivan Kondratov, Rustam Iminov, Andrii Khairulin, Yaroslav Mykhalonok, Anton Pochepko, Volodymyr Chashka-Ratushnyi, Iaroslava Kos, Stefano Moro, Matthieu Montes, Pengyu Ren, Jay W. Ponder, Louis Lagardere, Jean-Philip Piquemal, Davide Sabbadin
Summary: We report a computationally driven discovery of new SARS-CoV-2 main protease (M-pro) inhibitors, whose potency has been significantly improved from initial non-covalent ligands to final covalent compound. The study highlights the power of structure-based computational strategies for drug design and provides insights for further optimization of M-pro inhibitors.
Article
Chemistry, Physical
Chunyu Li, Juan Carlos Verduzco, Brian H. Lee, Robert J. Appleton, Alejandro Strachan
Summary: The response of materials to shock loading is crucial for planetary science, aerospace engineering, and energetic materials. Deep learning is used to predict the resulting shock-induced temperature fields in composite materials, achieving higher accuracy and lower computation cost compared to current state of the art techniques.
NPJ COMPUTATIONAL MATERIALS
(2023)
Article
Computer Science, Interdisciplinary Applications
Abdul Ahad Faizan, Osman Kirtel, Erkan Celebi, Abdullah Can Zulfikar, Fatih Goktepe
Summary: This study evaluates the impact of high-speed trains on environmental vibrations and proposes simplified computational models to validate the test results. The findings suggest that the ground vibrations induced by high-speed trains have a significant effect on the surrounding soil, especially in soft, medium, and dense soil areas.
COMPUTERS AND GEOTECHNICS
(2022)
Article
Biochemical Research Methods
Marina P. Oliveira, Philippe H. Huenenberger
Summary: The CombiFF scheme is a workflow for automated calibration of force-field parameters, which considers entire classes of organic molecules and their molecular topologies. It has been applied to the design of GROMOS-compatible united-atom force fields for different types of compounds and has shown good agreement with experimental data for various properties.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Article
Multidisciplinary Sciences
Zhifeng Kuang, John Luginsland, Robert J. Thomas, Patrick B. Dennis, Nancy Kelley-Loughnane, William P. Roach, Rajesh R. Naik
Summary: The application of electric fields in specific directions, especially in the direction perpendicular to the protein axis, can effectively denature the SARS-CoV-2 virus, providing a potential strategy for preventing its spread.
SCIENTIFIC REPORTS
(2022)
Article
Nanoscience & Nanotechnology
Nadav Zimron-Politi, Ryan C. Tung
Summary: In this paper, we validate an experimental model of contact resonance atomic force microscopy designed for sensors with long, massive tips. We develop a new technique and graphical method for identifying unknown system parameters and experimentally validate both the technique and the contact resonance model. Our contact resonance experimental measurements show a minimal error of 1.4%-4.5% compared to values obtained from nanoindentation, demonstrating the accuracy of the new model and parameter identification technique.
Article
Biochemistry & Molecular Biology
Malik Hisamuddin, Irum Rizvi, Ajamaluddin Malik, Faisal Nabi, Md Nadir Hassan, Syed Moasfar Ali, Javed Masood Khan, Tabish H. Khan, Rizwan H. Khan
Summary: This study provides insights into the pH-dependent conformational changes of DENV protease and its potential in facilitating the design of a therapeutic strategy for dengue fever.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Applied
Ting Zhang, Yixin Yuan, Jiale Chai, Xinling Wu, Ramesh Kumar Saini, Jingbo Liu, Xiaomin Shang
Summary: This study found that the addition of highly charged dextran sulfate (DS) can induce egg white protein (EWP) to form transparent hydrogel with better gelation properties. DS significantly prevents the formation of large insoluble aggregates of EWP during heating, which is necessary for forming a transparent gel. The EWP/DS hydrogel has higher gel strength and water holding capacity, and shows a highly ordered fibrous mesh structure after heat treatment.
FOOD HYDROCOLLOIDS
(2022)
Article
Food Science & Technology
Qingguan Liu, Yuxue Sun, Jianjun Cheng, Xiaonan Zhang, Mingruo Guo
Summary: Modification of food proteins by interactions with polyphenols can improve their functional properties. This study demonstrated that non-covalent complexation of soy isoflavones and whey proteins significantly increased the solubility of soy isoflavones and induced changes in the conformation and functionality of whey proteins. The findings provide useful information for the modification of whey proteins by polyphenols complexation.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Physics, Multidisciplinary
Garret Moddel, Ayendra Weerakkody, David Doroski, Dylan Bartusiak
Summary: The differential conductance of metal-insulator-metal devices increases when joined with Casimir cavities due to an imbalance in injection of hot charge carriers. Thinner cavities suppress more quantum vacuum modes and result in an observed increase in conductance. Changes in conductance with insulator thickness and other device parameters are consistent with an imbalance-induced injection of hot carriers. Additionally, anomalous offsets in current and voltage are observed, which are interpreted as a limit to the injection of hot carriers from zero-point fluctuations similar to a Delta E Delta t uncertainty principle.
PHYSICAL REVIEW RESEARCH
(2021)
Article
Chemistry, Physical
Maisa Vuorte, Susanna Kuitunen, Paul R. Van Tassel, Maria Sammalkorpi
Summary: An equilibrium state model is presented for the aggregation and adsorption of colloidal assemblies in apolar solvents, based on the step-wise aggregation response of fatty acids and monoglycerides in bio-oils. The model captures surface crowding and demonstrates the sensitivity of key observables to model parameters. Fits to molecular modelling data reveal that the model accurately reproduces chemically specific aggregate exponential distributions. The model provides an easily accessible means to estimate colloidal assembly and adsorption in oil environments.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Chemistry, Medicinal
Marta Stolarek, Aleksandra Pycior, Piotr Bonarek, Malgorzata Opydo, Elzbieta Kolaczkowska, Kamil Kaminski, Andrzej Mogielnicki, Krzysztof Szczubialka
Summary: In this study, the substitution of heparin with a photoswitch was investigated. The trans-cis and cis-trans photoisomerizations of the photoswitch resulted in changes in the hydrodynamic diameter of heparin and attenuated its anticoagulative properties.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Adam L. Harmat, Maria Morga, Jodie L. Lutkenhaus, Piotr Batys, Maria Sammalkorpi
Summary: Streaming potential and quartz crystal microbalance measurements were used to investigate the pH dependency of the adsorption of poly-L-lysine (PLL) and poly-L-arginine (PARG) on alpha-quartz surface, which was further supported by all-atom molecular dynamics simulations. The adsorption behavior was determined by the change in the number of peptide-surface ion pairs and the repulsive electrostatic interactions between the polypeptides. Low pH favored strong adsorption and stable monolayers, while high pH resulted in weakly bound but denser peptide films with limited stability. Electrostatic interactions, hydrogen bonding, and non-specific interactions played important roles in the adsorption process.
APPLIED SURFACE SCIENCE
(2023)
Article
Biochemical Research Methods
Klaudia Arciszewska, Ewa Kowalska, Filip Bartnicki, Piotr Bonarek, Agnieszka Katarzyna Banas, Wojciech Strzalka
Summary: Affinity chromatography (AC) is widely used for the purification of recombinant proteins. This study developed and characterized an AC system based on the specific and reversible interaction between a DNA aptamer and a lysine tag (Lys-tag) for the purification of recombinant proteins. The system was successfully applied to purify recombinant proteins from E. coli total protein extracts.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Chemistry, Physical
Sousa Javan Nikkhah, Maria Sammalkorpi
Summary: Hypothesis: Multicore block copolymer aggregates undergo self-assembly, leading to the spontaneous phase separation of the polymer system into multiple droplet-like cores with different compositions. These multicore aggregates are highly versatile and find applications in drug transport, catalysis, controlled solvation, and chemical reactions. The study investigates the influence of polymer system composition on the self-assembly process and proposes guidelines for polymer system design to achieve desired multicore assemblies. Simulations: Dissipative Particle Dynamics (DPD) simulations are used to study the self-assembly of a mixture of solvophobic homopolymers, an amphiphilic block copolymer, and a solvent. The assembly response and aggregate structure are analyzed in terms of block copolymer concentration, polymer component ratios, and chain length of the solvophobic homopolymer. Findings: The amount of block copolymer is crucial for controlling the formation of multicore or single core aggregates. A critical copolymer concentration specific to the polymer system is identified for multicore aggregation, and a minimum level of incompatibility between the solvent and the solvophobic component is required for multicore assembly. The study provides insights into tuning assembly from multicore aggregation to single core core-shell particles and offers guidelines for designing polymer systems to achieve multicore aggregates.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Physics, Multidisciplinary
Hossein Vahid, Alberto Scacchi, Maria Sammalkorpi, Tapio Ala-Nissila
Summary: Multivalent ions in polyelectrolyte solutions cause electrostatic correlations that can alter ion distributions and interactions. Our simulations demonstrate that ion shape and concentration, in addition to valency, can control rigid like-charged polyelectrolyte interactions. We show a correlation between the orientation of aspherical ions and the induced polyelectrolyte attraction through multivalency. This external control over interaction type, strength, and range can guide the self-assembly of like-charged polyelectrolytes.
PHYSICAL REVIEW LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Christopher Jonkergouw, Pihla Savola, Ekaterina Osmekhina, Joeri van Strien, Piotr Batys, Markus B. Linder
Summary: This study explores the chemical space of QS signaling molecules, defines the performance of different signals and ligands, and discovers a set of orthogonal intercellular QS signaling systems, expanding the toolkit for engineering community-wide behavior.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Piotr Bonarek, Dorota Mularczyk, Joanna I. Loch, Katarzyna Kurpiewska, Marta Dziedzicka-Wasylewska
Summary: This study evaluated the role of two mutations (L39Y and L58F) in the binding of beta-lactoglobulin to topical anesthetic pramoxine (PRM). Various techniques were used to understand the mechanisms of BLG-PRM interactions. The results showed that the L58F and L39Y mutations significantly increased the affinity to PRM, and the double mutant L39Y/L58F had an 80-fold increase in affinity compared to the natural protein BLG.
JOURNAL OF MOLECULAR RECOGNITION
(2023)
Article
Chemistry, Multidisciplinary
Sakari Lepikko, Ygor Morais Jaques, Muhammad Junaid, Matilda Backholm, Jouko Lahtinen, Jaakko Julin, Ville Jokinen, Timo Sajavaara, Maria Sammalkorpi, Adam S. Foster, Robin H. A. Ras
Summary: This study challenges the traditional assumption of surface heterogeneity as the major factor that affects the motion of liquid droplets on solid surfaces. It reveals a counterintuitive mechanism of slipperiness that is not expected based on the chemical heterogeneity of the surface. This finding opens up new avenues for enhancing the mobility of droplets.
Article
Chemistry, Physical
Tuuva Kastinen, Dawid Lupa, Piotr Bonarek, Dmitrii Fedorov, Maria Morga, Markus B. Linder, Jodie L. Lutkenhaus, Piotr Batys, Maria Sammalkorpi
Summary: We demonstrate that pH significantly affects the assembly mechanism and properties of PLL and PGA complexes through a combination of experimental characterization and molecular simulations. Various techniques, including DLS, LDV, ITC, CD, and AUC, are employed to assess the complexation, charge state, thermodynamics, secondary structure, and molecular weights of the peptides. Molecular dynamics simulations provide insights into the binding changes and hydrogen bonding involved in the complex formation. Our findings reveal the pH dependency of PLL/PGA complexation and highlight the potential of pH control in designing peptide materials.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Physics, Fluids & Plasmas
Xiang Yang, Sahin Buyukdagli, Alberto Scacchi, Maria Sammalkorpi, Tapio Ala-Nissila
Summary: EP mobility reversal refers to the phenomenon where the direction of polymer drift driven by an external electric field is reversed due to the change in sign of the counterion-dressed surface charge. In order to understand this counterintuitive effect, a strong-coupling-dressed Poisson-Boltzmann approach is applied to the cylindrical geometry of the polyelectrolyte-salt system. The derived analytical polymer mobility formula predicts that the increment of monovalent salt, the decrease of multivalent counterion valency, and the increase of the dielectric permittivity of the solvent suppress charge correlations and increase the concentration of multivalent bulk counterions required for EP mobility reversal. Coarse-grained molecular dynamics simulations support these predictions and show the induction of mobility inversion by multivalent counterions at dilute concentrations.
Article
Biochemistry & Molecular Biology
Dmitry A. Tolmachev, Maaria Malkamaki, Markus B. Linder, Maria Sammalkorpi
Summary: This study systematically characterizes the effects of ethanol on spider silk proteins by combining large-scale atomically-detailed molecular dynamics simulations and experiments. Ethanol promotes ordered structure in the protein molecules, leading to increased helix content and turns but also increased aggregation. The ethanol interacts with the hydrophobic regions of the spider silk protein, decreasing the hydrophobic interactions. Additionally, the protein solutes alter the microstructure of water/ethanol mixtures, reducing the level of larger local clustering.
Article
Chemistry, Multidisciplinary
Dmitrii Fedorov, Nelmary Roas-Escalona, Dmitry Tolmachev, Adam L. Harmat, Alberto Scacchi, Maria Sammalkorpi, A. Sesilja Aranko, Markus B. Linder
Summary: This study demonstrates the importance of weak interactions in the formation of condensates and provides a principle for rational protein design. By using a triblock approach, the propensity for condensate formation can be controlled by varying the weak dimerization of terminal blocks. The dissociation constants of the terminal domains directly correlate with the tendency for liquid-liquid phase separation. Additionally, differences in physical properties can be understood from the properties and interplay of constituent blocks.
Article
Chemistry, Physical
Maisa Vuorte, Aapo Lokka, Alberto Scacchi, Maria Sammalkorpi
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)