Article
Biochemistry & Molecular Biology
Michael Blaber
Summary: Symmetric protein architectures have aesthetic appeal and practical value in computational design, with the role of symmetry in hydrophobic core-packing cooperativity remaining underexplored. The threefold rotational symmetry in the beta-trefoil structure promotes cooperative core-packing interactions, ensuring stability and offering optimization solutions.
Article
Chemistry, Analytical
Neil Taylor, Wanli Ma, Adam Kristopeit, Sheng-Ching Wang, Andrew L. Zydney
Summary: A new analytical hydrophobic interaction chromatography method was investigated for evaluating the hydrophobicity of nanoparticles, showing good agreement with literature values. The method was used to evaluate the hydrophobicity of various nanoparticles, including a live attenuated viral vaccine, under different conditions. This new method can be implemented on any liquid chromatography system, providing accurate measurements in a short amount of time while avoiding the use of organic solvents.
ANALYTICAL CHEMISTRY
(2022)
Article
Construction & Building Technology
Hao Zhang, Song Mu, Jingshun Cai, Qi Ma, Jinxiang Hong, Jiawei Wang, Fengyin Du
Summary: This paper analyzes the influence of carboxylic acid ammonium salt on the hydrophobicity of cement-based materials and investigates its effects on hydrophobicity, moisture diffusion, and hydration products through experimental methods. The results show that the addition of carboxylic acid ammonium salt increases pore volume, and proposes an analytical hydrodynamic model to analyze the relationship between pore characteristic parameters and cementitious materials permeability.
CONSTRUCTION AND BUILDING MATERIALS
(2022)
Article
Chemistry, Physical
S. E. Perez-Figueroa, Andres Gallegos-Lozano, Carlos Mendoza
Summary: This study explores the non-trivial structures formed by the assembly of repulsive core-corona particles on a spherical surface. Monte Carlo simulations are used to investigate the equilibrium configurations at low temperatures, revealing a variety of minimal-energy arrangements including anisotropic and chiral structures. Different phase diagrams are constructed to study the influence of the size of the confining surface and the temperature on the configurations. The study also discusses the assembly of Platonic and Archimedean solids and the emergence of helical structures.
Article
Computer Science, Artificial Intelligence
Rumana Nazmul, Madhu Chetty, Ahsan Raja Chowdhury
Summary: This paper presents an approach to incorporate domain knowledge based on the concept of maximal 'core' formation into Memetic Algorithms for improving Protein Structure Prediction (PSP). By estimating and integrating the knowledge of maximal Hydrophobic core into the algorithm, the proposed approach shows superior performance in terms of convergence speed and minimal energy compared to existing methods.
KNOWLEDGE-BASED SYSTEMS
(2021)
Article
Agricultural Engineering
Chuanwei Zhang, Pengfei Zhang, Yanhui Li, S. Nair Sandeep, Jianyong Li, Maocheng Ji, Sixian Peng, Ning Yan, Fangyi Li
Summary: Through a single-sided cavity free-form foaming process, composites similar to wood cells were obtained using corn starch, pulp fiber, and sisal fibers as the middle layer. The composites were then coated with lignin-containing nanocellulose fibrils from pine bark to provide a wood bark-like barrier. The water barrier, mechanical property, apparent density, heat insulation, and biodegradability of the sandwich structured bio-composites were characterized. The results showed high water contact angle, low apparent density, and good tensile strength for the bio-composites, as well as significant biodegradability.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Engineering, Environmental
Shuangchun Lu, Qingling Liu, Rui Han, Jiaqi Shi, Miao Guo, Chunfeng Song, Na Ji, Xuebin Lu, Degang Ma
Summary: This study reports a strategy to synthesize Y zeolite and hydrophobic organic polymer core-shell composites, significantly improving the hydrophobicity and toluene adsorption capacity of Y zeolite. The composite exhibits excellent adsorption performance under both dry and wet conditions, suitable for practical applications. Such composite strategy can be applied to other zeolites for hydrophobic modification, increasing the adsorption capacity under wet conditions.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Chemistry, Physical
Namachivayam Karthik, Bruno Trindade, Nazanin Emami
Summary: Hydrophobic composites are prepared by encapsulating onion-like carbon on the surface of Ultra High Molecular Weight Polyethylene using a solvent-free mechanochemical process, resulting in increased water contact angle.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Polymer Science
Michael Ioelovich
Summary: The hydrophobicity of cellulose can be significantly increased through acid hydrolysis and esterification. Esterification disrupts the crystalline structure of cellulose, replacing polar hydroxyl groups with non-polar substituents to enhance the hydrophobicity. Increasing the number of non-polar groups in the ester substituent contributes to the rise in hydrophobicity of cellulose derivatives.
Article
Materials Science, Ceramics
Yeye Liu, Leilei Zhang, Fei Zhao, Chang Li, Hongchao Sheng, Hejun Li
Summary: A new type of highly flexible, fire-resistant and hydrophobic paper based on Si3N4 nanowires and polydimethylsiloxane (PDMS) is reported. The Si3N4@PDMS core-shell nanowires with 3D interlocking structure are designed, in which the Si3N4 nanowires act as the inorganic fire-resistant frameworks and the PDMS shell provides the hydrophobic surface. The obtained Si3N4@PDMS paper has the characteristics of writability, fire-resistance and hydrophobicity.
CERAMICS INTERNATIONAL
(2023)
Article
Chemistry, Physical
M. Pilkowski, G. Morgiante, J. Mysliwiec, M. Kuchowicz, J. Marczak
Summary: Surface wettability is crucial in coating science, and developing non-wettable materials has promising applications. Research on vapor phase modification of glass and silica substrates provided insight into chemical composition, roughness changes, and the effects of temperature and humidity on modified surfaces. Conducted studies contribute to a deeper understanding of surface properties and environmental durability of modified materials such as nanocomposites and coatings.
SURFACES AND INTERFACES
(2021)
Article
Chemistry, Physical
Hongyu Dong, Yingqing Zhan, Yiwen Chen, Yinlong Li, Ao Sun, Ximin Chen, Fei Zhu, Hongshan Jia
Summary: In this study, a hydrophobic and anticorrosive graphene oxide-based epoxy composite coating was developed using binary nano-fillers. The combination of graphene oxide and nano-silica improved the dispersion and compatibility of the epoxy coating, resulting in enhanced hydrophobicity and anti-corrosion performance.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2023)
Article
Agricultural Engineering
Maria Wennman, Anna J. Svagan, Marten Hellberg, Mikael S. Hedenqvist
Summary: Chemically bonded nonwovens are traditionally made with a latex binder containing plastic polymer and cellulosic fibers. However, they have low biodegradability and cannot be recycled. In this study, a biobased binder (PEC) made from carboxymethyl cellulose and chitosan dissolved in citric acid was combined with pea protein (PP) to create a fully biobased nonwoven with hydrophobic properties. By adjusting the fat content in PP and the protein content in the binder, different degrees of hydrophobicity and mechanical properties were achieved. The cured system showed a stable contact angle of around 120 degrees and significantly improved strength and stiffness compared to binder-free nonwovens in both dry and wet states.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Multidisciplinary Sciences
Ruchi Lohia, Matthew E. B. Hansen, Grace Brannigan
Summary: This study investigates the role of hydrophobicity on the functional impact of sequence variants in a genomewide context. The findings indicate that the functional impact is not correlated with the hydrophobicity of the SNP itself, but is strongly correlated with the size and minimum hydrophobicity of the contiguous hydrophobic sequence. The study also suggests that longer unbroken hydrophobic sequences are more likely to be under selection, leading to improvements in genomic tools and understanding of protein-aggregation disease etiology and protein evolutionary history.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Physics, Multidisciplinary
Mateusz Banach, Katarzyna Stapor, Piotr Fabian, Leszek Konieczny, Irena Roterman
Summary: Two slightly different forms of transthyretin show significantly different susceptibility to amyloid transformation process, with differences in hydrophobic core status and seed presence being the main factors.
Article
Biochemistry & Molecular Biology
Irena Roterman, Katarzyna Stapor, Krzysztof Gadek, Tomasz Gubala, Piotr Nowakowski, Piotr Fabian, Leszek Konieczny
Summary: This study characterized the structures of water-soluble proteins and membrane proteins using the fuzzy oil drop model. The analysis aimed to verify the potential use of an external force field in simulating the protein-folding process while considering the diverse nature of the environment that ensures a biologically active structure.
Article
Biochemical Research Methods
Katarzyna Stapor, Krzysztof Kotowski, Tomasz Smolarczyk, Irena Roterman
Summary: Protein secondary structure prediction is a crucial step in protein research. Conventional methods rely on evolutionary and protein sequence information, but require extensive computational resources. This study proposes a lightweight deep network approach that combines evolutionary information with new input features, resulting in shorter training and inference times. Furthermore, a new statistical methodology for evaluating prediction results is introduced.
BMC BIOINFORMATICS
(2022)
Article
Neurosciences
Werner Sommer, Katarzyna Stapor, Grzegorz Konczak, Krzysztof Kotowski, Piotr Fabian, Jeremi Ochab, Anna Beres, Grazyna Slusarczyk
Summary: This article introduces a new method (RESPERM) for detecting a single changepoint in a linear time series regression model. The study found that RESPERM detected changepoints with lower variance in time series with medium to large amounts of noise compared to the well-established SEGMENTED method. In practical applications, RESPERM is suitable for datasets with high noise levels.
Article
Biochemical Research Methods
Irena Roterman, Adam Sieradzan, Katarzyna Stapor, Piotr Fabian, Patryk Wesolowski, Leszek Konieczny
Summary: In computer simulations of protein folding, a module representing a polar solvent in water form was introduced. This module implements the fuzzy oil drop model (FOD), which uses a 3D Gauss function to express the presence of a polar environment and guide the folding process towards a hydrophobic core. Simulations using this model showed the presence of a hydrophobic core in the protein structures, even where it was absent in the native structure. The proposed modified FOD model (FOD-M) explains this phenomenon and highlights the importance of considering factors other than polarity in the folding environment.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2022)
Article
Biochemistry & Molecular Biology
Irena Roterman, Katarzyna Stapor, Piotr Fabian, Leszek Konieczny
Summary: This article investigates the structure and function of Connexins and pannexins proteins. Through comparative analysis, it is found that their hydrophobicity distribution and external force field characteristics are different, thus affecting their activity in different environments.
Article
Biochemistry & Molecular Biology
Irena Roterman, Katarzyna Stapor, Dawid Dulak, Leszek Konieczny
Summary: The experimentally determined structures of amyloid forms are primarily characterized by the two-dimensional forms of a single polypeptide chain, which is made possible by the beta structure and the numerous hydrogen bonds. This study proposes a possible mechanism for obtaining such a structure based on the geometric characterization of the polypeptide chain and molecular dynamics results. The potential mechanism of amyloid transformation is presented using transthyretin and amyloid A beta as examples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Irena Roterman, Katarzyna Stapor, Piotr Fabian, Leszek Konieczny
Summary: This paper analyzes the structure of the hydrophobic core in a collection of intrinsically disordered proteins (IDPs) and proposes an alternative classification method for intrinsically disordered regions (IDR) based on the ordering of the hydrophobic core.
Article
Multidisciplinary Sciences
Mateusz Banach
Summary: This paper demonstrates, discusses, and compares the effects of symmetrization in two calculation subroutines of the Fuzzy Oil Drop model for protein hydrophobicity density. The proposed modifications improve the accuracy, robustness, speed, and usability of the model, as confirmed by tests on various molecules with different shapes and functions.
Article
Engineering, Biomedical
Krzysztof Kotowski, Jeremi Ochab, Katarzyna Stapor, Werner Sommer
Summary: The study aims to assess the impact of ocular artifact removal on the single-trial N250 ERP analysis of face learning. By introducing a new semi-automatic approach, ocular artifact filtration significantly improved the regression modeling of single-trial ERP amplitudes, which is of great significance for the conclusions about the face learning process in individual participants.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2023)
Article
Biochemistry & Molecular Biology
Irena Roterman, Katarzyna Stapor, Leszek Konieczny
Summary: The amyloid structures in the PDB database are compared with their wild type forms. Amyloid fibrils have a 2D structure and a different hydrogen bond network compared to globular proteins. The beta-structure segments in amyloid fibrils have an anti-parallel system of hydrogen bonds. The conformational analysis of Phi and Psi angles reveals the presence of specific conditions and the correlation coefficient can indicate the distribution on the Ramachandran map.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Krzysztof Kotowski, Piotr Fabian, Irena Roterman, Katarzyna Stapor
Summary: Protein secondary structure prediction is crucial for understanding protein structure and function. The ProteinUnetLM model, based on a convolutional Attention U-Net architecture, achieves high prediction quality and inference times comparable to the best LSTM-based models without the need for time-consuming calculations. It outperforms LSTM-based predictors and shows potential for advancing the field.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Mateusz Banach
Summary: This paper presents an update to the ellipsoid profile algorithm (EP) which measures the globularity of protein structures without calculating molecular surfaces. The algorithm compares the volume of the voxelized representation of the atoms with the volume of voxels that can fit inside an enclosing ellipsoid. The updated EP algorithm includes an improved outlier detection subroutine based on principal component analysis, which enhances its performance in distinguishing between dense and disordered regions of molecules.
