Article
Biochemistry & Molecular Biology
Lijun Liang, Zhisen Zhang, Hongbo Wang, Jia-Wei Shen, Zhe Kong
Summary: Through more than 40 conductance events from microsecond molecular dynamics simulation, soft knock-on ion permeation mediated by water molecules in sodium channels was observed and confirmed. The change of average distance between four oxygen atoms in Glu177-Glu177 was found to play a crucial role in Na+ ion permeation. Exploration of the ionic conductance mechanism may guide the design of ion channel targeted drugs.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Multidisciplinary Sciences
Lianghao Guo, Wenfei Bo, Kaicheng Wang, Shaomeng Wang, Yubin Gong
Summary: The study investigates the interaction of terahertz waves with ions in nerve cell channels and its potential effects. It finds that terahertz radiation can generate electromagnetic radiation in calcium channels and accelerate the transport of calcium ions. These findings provide a theoretical basis for the future application of terahertz waves in neurological treatments.
Article
Chemistry, Physical
Miriam Jaeger, Thorsten Koslowski, Steffen Wolf
Summary: Ion channels play an important role in physiological information transfer and functional control. By using dissipation-corrected targeted molecular dynamics with Langevin equation simulations, the study investigated potassium diffusion through the gramicidin A channel and found coupled protein-ion dynamics during ion transfer. The results show that dissipation-corrected free energy profiles align well with predictions from other biased simulation methods, and the incorporation of an external electric field in Langevin simulations can predict macroscopic observables in the form of I-V characteristics.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Namho Kim, Ji Hye Lee, Yeonho Song, Jeong-Hyung Lee, George C. C. Schatz, Hyonseok Hwang
Summary: The effect of protonation state of glutamic acid on its translocation through cyclic peptide nanotubes (CPNs) was studied using molecular dynamics simulations. The study found that the protonation state of glutamic acid significantly influenced its transport through CPNs, as determined by the permeability coefficients. The potential of mean force calculations showed that the protonation state resulted in different free energy barriers, while the position-dependent diffusion coefficient profiles showed similar frictional behaviors.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Chiara Panosetti, Simon B. Annies, Cristina Grosu, Stefan Seidlmayer, Christoph Scheurer
Summary: Lithium ion batteries are crucial components in consumer electronics and emerging fields like electric mobility and renewable energy storage. The complex intercalation process in graphite anodes limits the charging speed and longevity of batteries, highlighting the need for better understanding and optimization of materials and mechanisms. By using simulation frameworks and optimizing parameters, researchers are able to accurately reproduce experimental results and study structural properties and diffusion barriers in lithium-intercalated graphite systems.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Engineering, Marine
Y. X. Qian, B. Teng
Summary: In this paper, an analysis is conducted on a 2D structural corner using an analytic local solution. The spatial derivative of the velocity potential is modified and accurately calculated. The results show that the near-field method has high precision in calculating the second-order force components compared to the conservative higher-order boundary element method.
Article
Medicine, Research & Experimental
Eduardo R. Almeida, Priscila V. Z. Capriles Goliatt, Heilio F. Dos Santos, Fabien Picaud
Summary: This study reveals that encapsulating cisplatin into carbon nanohorns (CNH) is a promising nanoformulation for targeted drug delivery to tumor sites. Biased molecular dynamics simulations show a four-stage mechanism of transmembrane transport, with the insertion stage potentially enhancing the retention of cisplatin in tumor sites.
MOLECULAR PHARMACEUTICS
(2023)
Article
Chemistry, Multidisciplinary
Van A. Ngo, Maria Queralt-Martin, Farha Khan, Lucie Bergdoll, Jeff Abramson, Sergey M. Bezrukov, Tatiana K. Rostovtseva, David P. Hoogerheide, Sergei Yu Noskov
Summary: The voltage-dependent anion channel (VDAC) responds to transmembrane potential by gating, and the residue K12 is responsible for its voltage sensitivity.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Olivera Drecun, Cecilia Bernardini, Misbah Sarwar, Alberto Striolo
Summary: This study investigates the interactions and agglomeration of γ-alumina nanoparticles in water and salt solutions. Molecular dynamics simulations are used to characterize surface effects, and dynamic light scattering experiments are conducted to study agglomeration at the macroscale. The results highlight the capability of molecular simulations to explain macroscopic observations.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2023)
Article
Cell Biology
Birthe Bernicke, Nils Engelbogen, Katharina Klein, Jeanette Franzenburg, Christoph Borzikowsky, Christian Peters, Ottmar Janssen, Ralf Junker, Ruben Serrano, Dieter Kabelitz
Summary: Vitamin D-3 has immunomodulatory effects and may contribute to seasonal variation of immune cells, particularly gamma delta T cells. This study found higher proportions of gamma delta T cells in winter compared to summer. Oral vitamin D-3 supplementation was associated with lower gamma delta T cell proportions, especially in spring. However, gamma delta T cell frequency did not directly correlate with serum levels of 25(OH)D-3. The active metabolite 1 alpha,25(OH)(2)D-3 inhibited the in vitro activation of gamma delta T cells.
Article
Physics, Applied
Madeleine Schroeder, Ximo Gallud, Elaine Petro, Oliver Jia-Richards, Paulo C. Lozano
Summary: In this study, coordinated molecular dynamics, ion cluster acceleration, and retarding potential analysis simulations were performed to investigate cluster fragmentation behavior in electrosprays. Molecular dynamics simulations were used to determine the fragmentation rates of ionic liquid clusters under different conditions. A simplified model of electrospray cluster acceleration was developed and used to simulate retarding potential analysis curves. The results obtained from the simulations were in good agreement with previous analysis, demonstrating the effectiveness of the coordinated molecular dynamics and retarding potential analysis approach in inferring electrospray beam parameters.
JOURNAL OF APPLIED PHYSICS
(2023)
Article
Biochemical Research Methods
Justyna D. Krys, Dominik Gront
Summary: Understanding protein structure and dynamics is crucial for investigating biological processes. We propose a novel hydrogen bond energy function for coarse-grained simulations, which accurately recognizes hydrogen bonds and identifies β-sheet structures in amyloid peptide simulations.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Article
Chemistry, Physical
Linus C. Erhard, Jochen Rohrer, Karsten Albe, Volker L. Deringer
Summary: By combining density-functional theory with machine-learning-based methods, we have developed accurate models for describing different forms of silica. This research is important for further understanding the atomic structure and properties of silica materials.
NPJ COMPUTATIONAL MATERIALS
(2022)
Article
Thermodynamics
Sonanki Keshri, Ujwala N. Patil
Summary: We studied the effects of salt concentration and solvent composition on the structure of sodium chloride solutions under supercritical conditions. The depth of contact ion pairs and solvent shared ion pairs increased with methanol content in the mixture and decreasing salt concentration. In solutions with low salt concentration, all ions formed one cluster, while smaller clusters of variable sizes were formed at higher salt concentrations. The cluster size distribution strongly depended on salt concentration and had a less pronounced effect on solvent composition.
FLUID PHASE EQUILIBRIA
(2021)
Review
Materials Science, Multidisciplinary
Xiao Zhang, Guanghui Ma, Wei Wei
Summary: Understanding how the properties of nanoparticles affect their interactions with cell membranes is crucial for their biomedical applications, and simulations are useful in providing atomic-level accuracy for dynamic changes in structure to reveal the mechanisms of nano-bio interface interactions.
NPG ASIA MATERIALS
(2021)
Article
Chemistry, Medicinal
Gerard Martinez-Rosell, Silvia Lovera, Zara A. Sands, Gianni De Fabritiis
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
Chemistry, Medicinal
Alejandro Varela-Rial, Maciej Majewski, Alberto Cuzzolin, Gerard Martinez-Rosell, Gianni De Fabritiis
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
Chemistry, Medicinal
Pablo Herrera-Nieto, Adria Perez, Gianni De Fabritiis
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
Chemistry, Physical
Adria Perez, Pablo Herrera-Nieto, Stefan Doerr, Gianni De Fabritiis
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2020)
Article
Chemistry, Physical
Stefan Doerr, Maciej Majewski, Adria Perez, Andreas Kramer, Cecilia Clementi, Frank Noe, Toni Giorgino, Gianni De Fabritiis
Summary: TorchMD is a molecular simulation framework that utilizes both classical and machine learning potentials. It allows for various force computations and supports learning and simulating neural network potentials. Through validation, it has been proven to be a useful toolkit for molecular simulations with machine learning potentials.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Review
Chemistry, Multidisciplinary
Alejandro Varela-Rial, Maciej Majewski, Gianni De Fabritiis
Summary: Virtual screening methods, such as molecular docking and physical-based molecular simulations, offer different advantages and limitations in drug discovery. While molecular docking provides fast results using approximations, physical-based simulations offer more accurate models but require expensive computing infrastructure. Both approaches are useful for solving different aspects of the drug discovery process.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Laura Marruecos, Joan Bertran, Daniel Alvarez-Villanueva, Maria Carmen Mulero, Yolanda Guillen, Luis G. Palma, Martin Floor, Anna Vert, Sara Arce-Gallego, Irene Pecharroman, Laura Batlle, Jordi Villa-Freixa, Gourisankar Ghosh, Anna Bigas, Lluis Espinosa
Summary: I kappa Bs act as cytoplasmic inhibitors of NF-kB transcription factors. Phosphorylated and SUMOylated I kappa B alpha binds to histones H2A and H4, influencing chromatin association and transcriptional regulation in skin and intestine stem cells and progenitor cells. Dynamic binding of I kappa B alpha to chromatin is necessary for intestinal cell differentiation, providing insight into the restricted nuclear distribution of p-I kappa B alpha in specific stem cell compartments.
Article
Chemistry, Medicinal
Martin Floor, Kengjie Li, Miquel Estevez-Gay, Luis Agullo, Pau Marc Munoz-Torres, Jenn K. Hwang, Silvia Osuna, Jordi Villa-Freixa
Summary: Conventional MD simulations face challenges in obtaining converged results, leading to the widespread use of structure-based models (SBMs) as an alternative. SBMs simplify and focus on relevant aspects of physical processes, allowing for modification of force field definitions and parameters to cater to specific biophysical simulations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Medicinal
Alejandro Varela-Rial, Iain Maryanow, Maciej Majewski, Stefan Doerr, Nikolai Schapin, Jose Jimenez-Luna, Gianni De Fabritiis
Summary: In this study, the authors present a new application to visualize the contribution of each input atom to the prediction made by a convolutional neural network, aiding in the interpretability of such predictions. The results suggest that the model is able to learn meaningful chemistry signals from the data, but it has also exposed the inaccuracies of the current model, serving as a guideline for further optimization.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Genetics & Heredity
Gonzalo Hernandez, Xenia Ferrer-Cortes, Veronica Venturi, Melina Musri, Martin Floor Pilquil, Pau Marc Munoz Torres, Ines Hernandez Rodriguez, Maria Angels Ruiz Minguez, Nicholas J. Kelleher, Sara Pelucchi, Alberto Piperno, Esther Plensa Alberca, Georgina Gener Ricos, Eloi Canamero Giro, Santiago Perez-Montero, Cristian Tornador, Jordi Villa-Freixa, Mayka Sanchez
Summary: This article describes six new patients of non-HFE related hereditary hemochromatosis, with two families having novel nonsense mutations in the HFE2 gene and three families having mutations in the TFR2 gene. These rare cases highlight the importance of early molecular diagnosis in a specialized center to prevent serious clinical complications.
Article
Chemistry, Medicinal
Francesc Sabanes Zariquiey, Adria Perez, Maciej Majewski, Emilio Gallicchio, Gianni De Fabritiis
Summary: This study evaluates a relative binding free energy calculation method based on the alchemical transfer method (ATM). The results show that ATM is competitive in terms of speed and accuracy compared to traditional methods and can be applied with any potential energy function.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Pablo Herrera-Nieto, Adria Perez, Gianni De Fabritiis
Summary: Intrinsically disordered proteins participate in biological processes by folding upon binding to other proteins. However, the process of coupled folding and binding is still poorly understood. This study used a new approach to reconstruct the binding and folding process between disordered protein c-Myb and CREB-binding protein. The long-term dynamic process revealed that a short stretch of amino acids on c-Myb forms a folded α-helix during binding, and initial native contacts formed by leucine residues, especially Leu298-Leu302, facilitate the binding and folding of the rest of the peptide.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Oncology
Eva Quandt, Nuria Masip, Sara Hernandez-Ortega, Abril Sanchez-Botet, Laura Gasa, Ainhoa Fernandez-Elorduy, Sara Plutta, Joan Marc Martinez-Lainez, Samuel Bru, Pau M. Munoz-Torres, Martin Floor, Jordi Villa-Freixa, May C. Morris, August Vidal, Alberto Villanueva, Josep Clotet, Mariana P. C. Ribeiro
Summary: Through yeast two-hybrid screening, we identified 10 new atypical cyclin-CDK complexes, including an active complex between CDK6 and cyclin I (CCNI) against retinoblastoma protein. Upregulation of CCNI increased breast cancer cell proliferation in vitro and in vivo, similar to the effect of cyclin D upregulation, but this effect was abolished by CDK6 silencing or palbociclib treatment. CCNI downregulation led to a decrease in cell number and a reduction in the percentage of cells reaching S phase. CCNI upregulation was also associated with high expression of E2F target genes in cancer cell lines and breast cancer tissue samples.
MOLECULAR ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Syed Jawad Ali Shah, Qianqian Zhang, Jingjing Guo, Hongli Liu, Huanxiang Liu, Jordi Villa-Freixa
Summary: The microtubule-associated protein tau plays a critical role in the development and protection of the nervous system. Dysfunction and accumulation of tau in the brain can lead to various neurodegenerative diseases. This study reveals the detailed mechanism of acetylation-driven tau aggregation.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Chemistry, Physical
Carles Navarro, Maciej Majewski, Gianni De Fabritiis
Summary: Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended time scales. This study presents a methodology that utilizes molecular dynamics simulations and neural networks to train a model that can accurately simulate protein folding events. The method eliminates the need for extensive simulations or labeled data and showcases extrapolation capabilities.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
