Article
Multidisciplinary Sciences
Yipei Guo, Ariel Amir
Summary: Maintaining stable protein concentrations in cells is crucial for proper cellular functioning, with network topology playing a key role in ensuring stability constraints and shaping evolutionary processes.
NATURE COMMUNICATIONS
(2021)
Correction
Multidisciplinary Sciences
Yipei Guo, Ariel Amir
Summary: A correction to the paper has been published.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Haifan Gong, Yumeng Zhang, Chenhe Dong, Yue Wang, Guanqi Chen, Bilin Liang, Haofeng Li, Lanxuan Liu, Jie Xu, Guanbin Li
Summary: We propose a novel Global-Local Graph Neural Network powered by Unbiased Curriculum Learning for the Protein Thermodynamic Stability Prediction (PTSP) task. Our method utilizes a Siamese graph neural network to extract protein features before and after mutation. Additionally, a local feature transformation module is designed to focus on the mutated site. To address the bias in the model caused by noisy samples, an unbiased curriculum learning method is introduced. Experimental results show that our method outperforms advanced protein stability prediction methods and state-of-the-art learning methods for regression prediction tasks.
Article
Biochemistry & Molecular Biology
Judit Rodriguez, Arnau Dominguez, Anna Avino, Gigliola Borgonovo, Ramon Eritja, Stefania Mazzini, Raimundo Gargallo
Summary: Cytosine-rich DNA sequences can form i-motif structures, which have the potential to modulate gene expression in vivo. The stability of i-motif structures is low at neutral pH, but can be increased by adding neighboring moieties or DNA ligands. This study investigated the relative effects of these structural moieties and ligands on i-motif stabilization using spectroscopic techniques and multivariate data analysis methods. The results showed that the duplex is responsible for stabilizing the i-motif structure at neutral pH, while the T:T base pair has little effect. Among the selected DNA-binding ligands, the G-quadruplex ligand BA41 interacts with the duplex but shows little interaction and stabilization within the i-motif.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Physical
Rita Gelli, Lorenzo Briccolani-Bandini, Marco Pagliai, Gianni Cardini, Francesca Ridi, Piero Baglioni
Summary: This study investigates the impact of Mg2+ on the structure and stability of Mg-substituted ACP nanoparticles by preparing particles with tunable composition and crystallinity. Results show that the stability of particles depends on the degree of Mg2+ substitution in the clusters, offering useful guidelines for the preparation and design of AMCP particles.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Hisham M. Dokainish, Yuji Sugita
Summary: The study proposes a new approach, gREST_SSCR, for exploring open-closed conformational changes in multidomain proteins. By using this method, a wider conformational space is reached compared to conventional MD, while maintaining the stability of protein domains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Yanfen Lyu, Ruonan He, Jingjing Hu, Chunxia Wang, Xinqi Gong
Summary: Protein-protein interactions are crucial in life activities. This paper focuses on studying the tetramer protein complex interaction, including predicting the interaction between chains of the tetramer protein complex and predicting the tetramer protein complex interface residue pairs. The proposed models achieved promising results with an AUC value of 0.6263 for predicting chain interactions and an accuracy of 82.14% for predicting interface residue pairs.
FRONTIERS IN GENETICS
(2023)
Article
Pharmacology & Pharmacy
Zhixiang Cui, Chang Liu, Shuman Cui, Lu Qin, Xin Zhang, Jian Guan, Shirui Mao
Summary: Polyelectrolyte nanocomplex (PEC) embedded microparticles using CS/PVA as the composite matrix were fabricated for enhanced oral insulin delivery. Optimal properties were achieved with CS 50 kDa in the matrix, showing good stability, improved enzymatic stability, and enhanced mucus penetration. The CS/PVA 1:1 group exhibited the highest relative pharmacological availability of 6.80%.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2022)
Article
Biochemistry & Molecular Biology
Yang Yang, Jianjun Zhao, Lianjie Zeng, Mauno Vihinen
Summary: The stability of proteins plays a crucial role in various biological processes and applications. Experimental determination of protein stability has been challenging with limited data. In this study, a machine learning predictor, ProTstab2, was developed using limited proteolysis and mass spectrometry approaches to accurately predict the thermal stabilities of proteins. The ProTstab2 showed superior performance compared to previous methods, and it was applied to predict and compare the stabilities of proteins in human, mouse, and zebrafish proteomes. The tool is freely available for use.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Simone Marini, Marco Oliva, Ilya B. Slizovskiy, Noelle Robertson Noyes, Christina Boucher, Mattia Prosperi
Summary: Antimicrobial resistance (AMR) poses a significant and growing public health threat, requiring automatic identification of resistant bacterial strains. Research shows that known AMR protein variants tend to correspond to exposed residues, while susceptible counterparts tend to be buried. Based on these findings, a novel relative solvent accessibility-based AMR scoring system (RSA-AMR) has been developed to estimate the propensity of altering relative solvent accessibility of any protein variant, and potentially conferring or hindering AMR, providing a ten-fold increase in Specificity.
FRONTIERS IN GENETICS
(2021)
Article
Nanoscience & Nanotechnology
Siying Chen, Zhicheng Le, Jiayue Gu, Lixin Liu, Zhijia Liu, Yongming Chen
Summary: A small-molecule amphiphile molecular library was generated and screened, resulting in the identification of dimeric and trimeric amphiphiles for intracellular protein delivery. The trimeric amphiphile showed superior protein loading performance and delivery efficiency through the endocytosis pathway and subsequent endosomal escape. Moreover, the trimeric amphiphile was capable of delivering hard-to-deliver native antibodies into the cytosol. Overall, this well-designed and cost-effective amphiphile platform holds great promise for improving cytosolic protein delivery capacity.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Biochemistry & Molecular Biology
Thomas Attaribo, Gaiqun Huang, Xiangdong Xin, Qinlei Zeng, Yueyue Zhang, Ning Zhang, Liumei Tang, Rita-Cindy Aye-Ayire Sedjoah, Ran Zhang, Kwang Sik Lee, Byung Rae Jin, Zhongzheng Gui
Summary: The study demonstrated that the Spp-Glu conjugate could improve the thermal stability and antioxidant activity of cyanidin-3-O-glucose, forming complexes under different pH conditions to effectively attenuate degradation and enhance stability. Spectroscopic techniques revealed the formation of complexes via hydrophobic interactions and static quenching processes when C3G was bound to Spp or Spp-Glu, suggesting the potential of Spp-Glu in protecting and delivering anthocyanins during industrial applications for functional food formulation.
Article
Chemistry, Applied
Shuai Ren, M. Monica Giusti
Summary: Whey protein preheating temperature significantly affects the stability and antioxidant capacity of anthocyanin colorants, with the best performance observed at 50 degrees Celsius.
FOOD HYDROCOLLOIDS
(2022)
Article
Multidisciplinary Sciences
Francis Gaudreault, Christopher R. Corbeil, Traian Sulea
Summary: This study employs physics-based protein docking methods to construct a set of decoys and utilizes AlphaFold2's composite score to rescore docking poses, leading to significant improvements in antibody-antigen unbound docking performance. The benefits include increased early enrichment and improved ranking of medium-quality docking models.
SCIENTIFIC REPORTS
(2023)
Article
Engineering, Electrical & Electronic
Zhou Zhang, Zhenzhan Wang, Wenming He, Xiaolin Tong
Summary: Higher spatial resolution can enhance the application ability of spaceborne microwave radiometer data. The effect of enhanced field of view (FOV) and sampling strategy on spatial resolution improvement was analyzed using the Backus-Gilbert (BG) method, with the scanning parameters of the FengYun-3D Microwave Radiation Imager (MWRI) as an example. The results show that selecting an appropriate enhanced FOV and increasing the sampling overlap rate can reduce brightness temperature (BT) error and improve spatial resolution.
IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING
(2023)
Article
Biochemistry & Molecular Biology
Lorna J. Smith, Wilfred F. van Gunsteren, Niels Hansen
Summary: Using molecular dynamics simulations and order-parameter restraining MD simulations, a conformational ensemble consistent with experimental data on proteins can be obtained. Restraining S2CH parameters in methyl groups is found to be less reliable compared to S2NH order-parameter restraining due to assumptions and approximations used in deriving experimental values.
Article
Chemistry, Physical
Takeshi Kobayashi, Hamzeh Kraus, Niels Hansen, Maria Fyta
Summary: This study proposes a modeling approach for atomic-resolution studies of supported ionic liquid phase (SILP) catalytic systems in silica mesoporous confinement. By developing a force field for the Ru-based catalyst, investigating its solvation behavior in different solvents, and studying the properties of the confined system, important insights are gained for optimizing SILP systems.
Review
Chemistry, Physical
Wilfred F. van Gunsteren, Xavier Daura, Patrick F. J. Fuchs, Niels Hansen, Bruno A. C. Horta, Philippe H. Huenenberger, Alan E. Mark, Maria Pechlaner, Sereina Riniker, Chris Oostenbrink
Summary: Computer simulations of molecular systems play a crucial role in chemistry, biology, and physics, but it is important to consider uncertainty and errors affecting the calculated properties; advantages and shortcomings of commonly used assumptions and approximations in simulating bio-molecular systems should be taken into account; developers can improve simulation quality by discussing ways to facilitate and expand research involving bio-molecular simulations.
Article
Biochemistry & Molecular Biology
Lorna J. Smith, Wilfred F. van Gunsteren, Bartosz Stankiewicz, Niels Hansen
Summary: Experimental (3)J-coupling values derived from NMR on proteins are not straightforward for protein structure determination due to sensitivity and possibility of multiple values. However, by using a specific MD simulation method, it is possible to obtain a conformational ensemble compatible with experimental data, considering averaging and the algorithm's ability to escape local minima.
JOURNAL OF BIOMOLECULAR NMR
(2021)
Article
Chemistry, Physical
Hamzeh Kraus, Julia Rybka, Alexandra Hoeltzel, Nicole Trebel, Ulrich Tallarek, Niels Hansen
Summary: A software tool is presented for rapid model building of functionalised silica pores to study confinement effects in various applications. The tool allows selection of chemical structure and density, control of residual hydroxylation, and independent functionalisation of interior and exterior pore surfaces.
MOLECULAR SIMULATION
(2021)
Article
Chemistry, Applied
Christopher Kessler, Johannes Eller, Joachim Gross, Niels Hansen
Summary: A classical density functional theory (cDFT) based on the PC-SAFT equation of state is proposed for the calculation of adsorption equilibria in covalent organic frameworks (COFs). The results show excellent agreement between PC-SAFT DFT and GCMC simulations for adsorption isotherms in COFs, indicating the predictive power of the method in selective accumulation of longer hydrocarbons in binary mixtures.
MICROPOROUS AND MESOPOROUS MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
Daniel Markthaler, Hamzeh Kraus, Niels Hansen
Summary: This study employed umbrella sampling along a one-dimensional order parameter combined with Hamiltonian replica exchange to calculate the binding free energy of five guest molecules known to have affinity for cucurbit[8]uril. An empirical approach was proposed to correct for the overestimation of affinity by the GAFF force field, and subsequently applied to seven guest molecules in the Drugs of Abuse SAMPL8 challenge. While the systematic error decreased, quantitative agreement with experiment was only reached for a few compounds.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2022)
Article
Chemistry, Physical
Hamzeh Kraus, Niels Hansen
Summary: Immobilized p-cyclodextrin molecules in mesoporous silica support greatly enhance the uptake of benzene and p-nitrophenol from aqueous solution, exceeding theoretical binding capacity. In addition to 1:1 complexes, 1:2 and 1:3 host-guest complexes are formed during the adsorption process.
ADSORPTION-JOURNAL OF THE INTERNATIONAL ADSORPTION SOCIETY
(2022)
Article
Biophysics
Maria Pechlaner, Wilfred F. van Gunsteren, Niels Hansen, Lorna J. Smith
Summary: The study compares different methods of handling solvent molecules in protein simulations and finds that using explicit water molecules in molecular dynamics simulations provides more accurate modeling of experimental data compared to omitting water molecules. Omission of water molecules may lead to inaccuracies in protein conformation and dynamics simulations.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2022)
Article
Chemistry, Physical
Wilfred F. van Gunsteren, Maria Pechlaner, Lorna J. Smith, Bartosz Stankiewicz, Niels Hansen
Summary: A method for structure refinement of molecules based on residual dipolar coupling (RDC) data is proposed. It avoids the use of an alignment tensor and assumes that the overall rotation of the molecule is decoupled from its internal motions and that the molecule is rigid. The method demonstrates the influence of molecular flexibility and force-field deficiencies on the outcome of structure refinement based on RDCs.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Applied
Christopher Kessler, Robin Schuldt, Sebastian Emmerling, Bettina V. Lotsch, Johannes Kaestner, Joachim Gross, Niels Hansen
Summary: This study investigates the adsorption isotherms of gases in COF-LZU1 using molecular simulations and reveals the significant influence of the real structure on the adsorption properties.
MICROPOROUS AND MESOPOROUS MATERIALS
(2022)
Article
Multidisciplinary Sciences
Nils E. R. Zimmermann, Gabriela Guevara-Carrion, Jadran Vrabec, Niels Hansen
Summary: The study investigates the thermodiffusion behavior of binary Lennard-Jones mixtures in the liquid state by combining NEMD and EMD simulations. It finds that the Soret coefficient has a straightforward dependence on thermodynamic properties, but a more complex dependence on dynamic properties. The study identifies the limit of applicability of a popular theoretical model in thermodiffusion behavior research through uncertainty analysis.
ADVANCED THEORY AND SIMULATIONS
(2022)
Article
Chemistry, Physical
Hamzeh Kraus, Marc Hogler, Niels Hansen
Summary: Molecular dynamics simulations were conducted on solvent-filled cylindrical silica mesopores with a diameter of 5 nm to obtain a detailed understanding of the fluid structure and self-diffusion coefficient in confinement. Two approaches were compared to calculate the self-diffusion coefficient, and the ratio between the bulk and pore self-diffusion coefficient was obtained. This ratio, which reflects the influence of confinement on the fluid, was found to be between 2 and 3 for all solvent molecules studied, regardless of the computational approach or the type of silica used.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
