Article
Chemistry, Multidisciplinary
Tal Ben Uliel, Eliyahu M. Farber, Hagit Aviv, Wowa Stroek, Marilena Farbinteanu, Yaakov R. Tischler, David Eisenberg
Summary: Combining polarized low-frequency Raman spectroscopy with single crystal XRD, the study on barium nitrilotriacetate assigned Raman peaks experimentally and determined directional long-range interactions influencing fracture directions during crystallization. This established an important link between structural motifs in the precursor and the porosity of carbon yielded upon pyrolysis.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Wanda Niemyska, Pawel Rubach, Bartosz A. Gren, Mai Lan Nguyen, Wojciech Garstka, Fernando Bruno da Silva, Eric J. Rawdon, Joanna Sulkowska
Summary: AlphaKnot is a server that measures entanglement in AlphaFold-solved protein models while considering pLDDT confidence values. It provides a database and analysis functions for studying protein knotting. Entanglements are classified based on pLDDT confidence values and presented in a matrix diagram to show the knotting complexity and types.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Md Mahfuzur Rahaman, Nabila Shahnaz Khan, Shaojie Zhang
Summary: In this study, a method called RNAMotifComp is proposed to analyze the instances of well-known structural motif families and establish a relational graph among them. The relationships between these motif families are visualized using a designed method. The importance of RNAMotifComp is demonstrated through the validation of discovered correlations and the use of a Naive Bayes classifier.
Article
Chemistry, Multidisciplinary
Qianchen Liu, Alberto Perez
Summary: Integrins on the cell surface interact with functional motifs in the extracellular matrix (ECM), triggering biological actions like migration, adhesion, or growth. Computational tools have been limited in identifying novel binding motifs for integrin domains. Revisiting traditional and novel computational tools for the I-domain of the alpha 2 beta 1 integrin is important for improving their performance in identifying new binding motifs.
FRONTIERS IN CHEMISTRY
(2023)
Article
Biology
Markus Sutter, Cheryl A. Kerfeld
Summary: Bacterial microcompartments (BMCs) are protein-based organelles with unique shell proteins and selective permeability. We have developed a webserver tool using HMM profiles to analyze and categorize BMCs, providing users with information and a reference database.
Article
Chemistry, Medicinal
Valentina Sora, Matteo Tiberti, Ludovica Beltrame, Deniz Dogan, Shahriyar Mahdi Robbani, Joshua Rubin, Elena Papaleo
Summary: Due to the complex nature of noncovalent interactions and their long-range effects, analyzing protein conformations using network theory can be enlightening. However, there are limitations in the definition of network cutoffs, assessment of network stability, and available tools. Therefore, a common framework that promotes reproducibility and establishes common protocols in the Protein Structure Network (PSN) field would benefit the protein science community.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Aditya Mittal, Anandkumar Madhavjibhai Changani, Sakshi Taparia
Summary: This study identified unique signatures of intrinsic disorder by systematically synthesizing different peptide libraries, expanding the known intrinsically disordered proteins and providing a major advancement in exploring the functional manifestations of such proteins.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Review
Biochemistry & Molecular Biology
Valentina Sora, Elena Papaleo
Summary: This article provides an updated overview of the structural features characterizing BH3s and BH3-mediated interactions, focusing on human proteins. It elaborates on the plasticity of BCL2 proteins and motif properties, also discussing the implications of these findings for the discovery of interactors of the BH3-binding groove of BCL2 proteins and the design of mimetics for therapeutic purposes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Physical
Christopher C. Walker, Garrett A. Meek, Theodore L. Fobe, Michael R. Shirts
Summary: In this paper, a Python-based simulation framework, cg_openmm, is introduced for modeling coarse-grained hetero-oligomers and screening them for structural and thermodynamic characteristics. The framework includes tools for building topology, setting up simulations, and analyzing thermodynamic and structural properties. The capabilities of cg_openmm are demonstrated on a simple coarse-grained model, showing the formation of stable helices through cooperative folding transitions and the tunability of helix geometries and stabilities by manipulating force-field parameters.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Multidisciplinary Sciences
Vladimir R. Rudnev, Liudmila I. Kulikova, Anna L. Kaysheva, Alexander V. Efimov, Dmitry A. Tikhonov
Summary: This study investigated the stability of structural motifs using molecular dynamics, specifically focusing on alpha-alpha-corners. It was found that alpha-alpha-corners are autonomous structures stable in aquatic environments, through analysis of their geometric characteristics and torsion angles.
Article
Biochemistry & Molecular Biology
Kirill Sergeevich Nikolsky, Liudmila Ivanovna Kulikova, Denis Vitalievich Petrovskiy, Vladimir Removich Rudnev, Tatiana Vladimirovna Butkova, Kristina Akhmedovna Malsagova, Arthur Tigranovich Kopylov, Anna Leonidovna Kaysheva
Summary: In this study, we investigated the autonomous stability of three-helix bundle and SH3-type barrels outside the protein environment. Through molecular experiments and comparative analysis, we demonstrated the potential for reducing computational time and improving performance without significant loss of information.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Engineering, Electrical & Electronic
Yuhang Ma, Yunlong Zhao, Lu Liu, Ruiyu Bi, Xiaolong Zhu, Junbin Zang, Dong Guo, Jiuzhang Men, Zhidong Zhang, Chenyang Xue
Summary: Pulse wave provides detailed information about the cardiovascular system and is connected to various physiological changes. This study developed a fingertip-like pulse sensor based on a piezoresistive sensor, which can accurately extract weak pulse signals. The sensor has excellent performance in terms of linearity, hysteresis, and sensitivity. A pulse acquisition device was also developed and applied in clinical practice, demonstrating potential application in digital pulse diagnostics.
IEEE SENSORS JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Leonardo Salicari, Antonio Trovato
Summary: Researchers investigated the presence of entangled motifs in membrane protein structures and found that they occur at a similar frequency as in general proteins. However, the chirality bias of double-winding motifs is reversed in membrane proteins compared to general proteins. These observations may be explained by the differences in co-translational folding mechanisms between membrane and globular proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Mio K. Shibuta, Takuya Sakamoto, Tamako Yamaoka, Mayu Yoshikawa, Shusuke Kasamatsu, Noriyoshi Yagi, Satoru Fujimoto, Takamasa Suzuki, Satoshi Uchino, Yuko Sato, Hiroshi Kimura, Sachihiro Matsunaga
Summary: The study introduces a genetically encoded system called mintbody into Arabidopsis thaliana, allowing real-time quantitative measurement of endogenous modification level using a protein processing- and 2A peptide-mediated two-component system. This enables quantitative tracking of spatiotemporal dynamics of transcription, with observations of transcription level variations among tissues in the root and dynamic changes during the mitotic phase. The approach provides live visualization of transcription level in a single cell and enhances understanding of spatiotemporal transcription dynamics.
COMMUNICATIONS BIOLOGY
(2021)
Article
Mathematics
Alexander Churkin, Franziska Totzeck, Rami Zakh, Marina Parr, Tamir Tuller, Dmitrij Frishman, Danny Barash
Summary: This study conducted a mathematical analysis on a large dataset of RNA secondary structures in the coding regions of viruses using topological indices capturing Laplacian eigenvalues, with the aim of structural classification and identification of novel functional motifs. The analysis demonstrated the ability to extract structural categories such as stem-loop structures of different sizes based on RNA structure tree-graph representation, and it can potentially be applied beyond viral RNA structures to other biological agents involving RNA secondary structures.
