Article
Biochemical Research Methods
Alessio Del Conte, Alexander Miguel Monzon, Damiano Clementel, Giorgia F. Camagni, Giovanni Minervini, Silvio C. E. Tosatto, Damiano Piovesan
Summary: RING-PyMOL is a plugin for PyMOL that enhances the analysis and visualization of structural ensembles and molecular dynamic simulations. It combines residue interaction networks and structural clustering to provide a powerful tool for studying conformational complexity. It can identify correlating contacts, interaction patterns, and explain structural heterogeneity and molecular function. RING-PyMOL is easy to use, fast, and generates interactive plots and output files for further analysis.
Article
Multidisciplinary Sciences
Zhengwu Fang, Jianwei Xiao, Susheng Tan, Chuang Deng, Guofeng Wang, Scott X. Mao
Summary: This study observed the dynamic structural transformation of faceted grain boundaries (GBs) in gold nanocrystals during stress-driven GB migration using in situ high-resolution transmission electron microscopy combined with molecular dynamics simulations.
Article
Biochemistry & Molecular Biology
Tolga Aslana, Asli Yenenler-Kutlu, Umut Gerlevik, Ayse Cigdem Aktuglu Zeybek, Ertugrul Kiykim, Osman Ugur Sezermanb, Necla Birgul Iyisona
Summary: Phenylketonuria is an autosomal recessive disorder caused by mutations in the phenylalanine hydroxylase gene. Two novel mutations in the PAH gene, p.Y198N and p.Y204F, were found in a PKU patient. In-silico analyses and molecular dynamics simulations were used to investigate the impact of these mutations on the structural stability of the PAH enzyme. Results showed that these mutations may affect the spatial organization of catalytic residues and lead to fluctuations in the enzyme structure, potentially inhibiting dimerization and enzyme activation. Further studies are needed to fully understand the roles of these mutations in the etiology of PKU.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Subramee Sarkar, Swaroop Chandra, A. S. Suneesh, N. Ramanathan, K. Sundararajan, A. Suresh, N. Sivaraman
Summary: The behavior of different extractant-metal nitrate systems was studied through infrared spectroscopy and dynamic light scattering measurements, revealing the formation of metal nitrate-ligand complexes and the enrichment of 'trans' cluster of conformations in the organic phase. Conclusive evidence for preferential stabilization of 'trans' cluster of conformations in a polar environment was obtained from Density Functional Theory and IR spectroscopy, shedding light on the factors determining the sizes to which aggregates could grow in a given extractant-metal nitrate system.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Biology
Utsab R. Shrestha, Jeremy C. Smith, Loukas Petridis
Summary: The study demonstrates that enhancing the sampling using Hamiltonian replica exchange molecular simulation (HREMD) leads to accurate unbiased ensembles of intrinsically disordered proteins. Standard molecular simulation cannot reproduce small-angle scattering data as well as HREMD, highlighting the utility of the suggested approach.
COMMUNICATIONS BIOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Filip Formalik, Kaihang Shi, Faramarz Joodaki, Xijun Wang, Randall Q. Snurr
Summary: This article focuses on the role of atomic-level modeling in metal-organic framework (MOF) research, including key methods such as density functional theory, Monte Carlo simulations, and molecular dynamics simulations. These methods provide new insights into MOF properties, such as predicting structural transformations, understanding thermodynamic properties and catalysis, and providing information for classical simulations. The use of machine learning techniques in quantum and classical simulations is also discussed, which can enhance accuracy, reduce computational costs, and optimize MOF stability.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Chemistry, Physical
Liwei Chang, Alberto Perez, Ramon Alain Miranda-Quintana
Summary: The paper introduces new algorithms for classifying structural ensembles of macromolecules using extended similarity measures which reduce computational complexity. The approach captures larger ensembles and transitions between states, developing efficient techniques and a novel clustering algorithm utilizing the extended similarity indices. The new metrics are applied to analyze biological systems' ensembles, showing excellent performance and faster processing, with an efficient cost-function for merging clusters.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Materials Science, Multidisciplinary
Peng Dai, Kai Sun, Otto L. Muskens, C. H. de Groot, Ruomeng Huang
Summary: Dynamic structural color provides a time dimension to enhance information load and functionality. This study presents the inverse design of a dynamic structural color asymmetric Fabry-Perot cavity using parameter-based conditional generative adversarial networks. The designed structure achieves a large gamut and color coverage variation through the phase change of a VO2 layer.
OPTICAL MATERIALS EXPRESS
(2022)
Article
Engineering, Electrical & Electronic
Gustavo Zoireff, Diego Samaniego, Borja Vidal
Summary: A new photonic technique is presented for implementing both stopband and passband microwave filters, with high stopband rejection. By controlling polarization state and optoelectronic conversion, the filter response can be dynamically switched and has high application potential. Experiments show a very high stopband rejection of 67dB and the ability to dynamically change the filter response to implement a bandpass response.
IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS
(2021)
Article
Biochemistry & Molecular Biology
Lisa M. Pietrek, Lukas S. Stelzl, Gerhard Hummer
Summary: Disordered proteins and nucleic acids are important in cellular function and disease. This review discusses recent advances in computationally exploring the dynamics of flexible biomolecules. While molecular dynamics simulation has improved, large-scale computing resources and validation are needed for simulating full-length disordered biopolymers. Hierarchical chain growth is a computationally efficient alternative that combines chain fragments into detailed biomolecular structures. Applications to neurodegeneration-linked proteins highlight the use of hierarchical chain growth, and connections to AI-based structural modeling are also discussed.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Benjamin P. Kellman, Anne Richelle, Jeong-Yeh Yang, Digantkumar Chapla, Austin W. T. Chiang, Julia Najera, Bokan Bao, Natalia Koga, Mahmoud A. Mohammad, Anders Bech Bruntse, Morey W. Haymond, Kelley W. Moremen, Lars Bode, Nathan E. Lewis, Chenguang Liang, Annalee Furst
Summary: This study constructs a biosynthetic network for Human Milk Oligosaccharides (HMOs) using a systems biology framework and predicts the involved glycosyltransferases. The research provides a molecular basis for HMO biosynthesis, guiding progress in understanding and improving infant health and development.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
S. Sunidhi, Sukriti Sacher, Parth Garg, Arjun Ray, Atul
Summary: ATP binding cassette transporter A1 (ABCA1) is crucial for maintaining lipid homeostasis and cholesterol transport. Two theories of lipid efflux by ABCA1, the alternating access and lateral access, have been proposed. Recent studies using cryo-EM structure and molecular dynamics simulations have provided insights into the conformational changes of ABCA1 and its interactions with lipids in heterogeneous environments.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Chemistry, Physical
Linfeng Lan, Liang Li, Pance Naumov, Hongyu Zhang
Summary: Studies on organic optical waveguide materials have gained importance due to their advantages such as low optical losses and attractive optical properties. Flexible organic crystals have been developed, opening up opportunities for the design of flexible single-crystalline electronic devices. These crystals have been used in optical transmission and the development of various elastic organic crystals with different structures and functions, leading to the realization of self-doped crystal waveguides, three-dimensional optical waveguides, and other optical elements. The applications of these flexible organic crystals have also been extended to low/high-temperature environments and in combination with inorganic/polymeric materials, resulting in the development of new hybrid functional materials.
CHEMISTRY OF MATERIALS
(2023)
Article
Chemistry, Medicinal
Maximilian Meixner, Martin Zachmann, Sebastian Metzler, Jonathan Scheerer, Martin Zacharias, Iris Antes
Summary: Macrocycles are challenging molecules for computational modeling studies, but the accurate prediction of their bioactive conformations can be achieved through the optimization of sampling and docking processes.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemical Research Methods
Sylvain Trager, Giorgio Tamo, Deniz Aydin, Giulia Fonti, Martina Audagnotto, Matteo Dal Peraro
Summary: CLoNe is a Python-based clustering scheme built on the Density Peaks algorithm, which can extract meaningful conformations from structural ensembles regardless of cluster shape, size, distribution, and amount, and improves on the original algorithm in key aspects. It is applicable to membrane binding events, ligand-binding pocket opening, and the identification of dominant dimerization motifs or inter-domain organization.