Article
Multidisciplinary Sciences
Rita dos Santos Natividade, Melanie Koehler, Priscila S. F. C. Gomes, Joshua D. Simpson, Sydni Caet Smith, Diego E. B. Gomes, Juliette de Lhoneux, Jinsung Yang, Ankita Ray, Terence S. Dermody, Rafael C. Bernardi, Kristen M. Ogden, David Alsteens
Summary: This study investigates the nanomechanical properties of viral attachment proteins and their impact on virus-binding capacity and infectivity. The research reveals that conformational changes in the viral protein a1 significantly increase its affinity for JAM-A, leading to enhanced infectivity. The study also demonstrates how GM2 enhances the a1-JAM-A interaction. These findings provide important insights for the development of antiviral drugs and improved oncolytic vectors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Jiachen Li, Qi Wang, Yaoquan Tu
Summary: In this study, an advanced sampling technique was used to investigate the role of cleavage site sequences in prothrombin activation. The results suggest that the cleavage site at R320 is favored for prothrombin activation, and the binding between Pep320 and the FXa catalytic triad is more stable due to strong electrostatic interactions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Wanhao Cai, Miriam Jaeger, Jakob T. Bullerjahn, Thorsten Hugel, Steffen Wolf, Bizan N. Balzer
Summary: In this study, the rupture force and friction of the biotin-streptavidin complex under a externally applied force were investigated using AFM-based single molecule force spectroscopy and molecular dynamics simulations. Anisotropic friction, arising from an experimentally uncontrolled orientation parameter, was identified. The study suggests that anisotropic friction should be taken into account for a complete understanding of friction in biomolecular dynamics and anisotropic mechanical environments.
Article
Multidisciplinary Sciences
Q. F. He, J. G. Wang, H. A. Chen, Z. Y. Ding, Z. Q. Zhou, L. H. Xiong, J. H. Luan, J. M. Pelletier, J. C. Qiao, Q. Wang, L. L. Fan, Y. Ren, Q. S. Zeng, C. T. Liu, C. W. Pao, D. J. Srolovitz, Y. Yang
Summary: The development of high-performance ultraelastic metals is crucial for various industrial applications, and chemically complex alloys with large atomic size misfits have shown promising properties, including a high elastic strain limit and a constant elastic modulus at room temperature.
Article
Chemistry, Physical
J. E. Floyd, J. R. Lukes
Summary: A neural network-assisted molecular dynamics method has been developed to reduce the computational cost of open boundary simulations and accurately represent the effects of unmodeled surrounding fluid.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Andrew Jewett, David Stelter, Jason Lambert, Shyam M. Saladi, Otello M. Roscioni, Matteo Ricci, Ludovic Autin, Martina Maritan, Saeed M. Bashusqeh, Tom Keyes, Remus T. Dame, Joan-Emma Shea, Grant J. Jensen, David S. Goodsell
Summary: Coarse-grained models are crucial in studying biomolecular dynamics and assembly, but simulating them can be challenging due to unconventional force fields and particle attributes, as well as systems not being in thermal equilibrium. Moltemplate is a file format for storing coarse-grained molecular models and forces, with broad scope and popularity in computational chemistry, materials science, and structural biology. It accommodates new forces developed for LAMMPS, making it a useful tool with thousands of users.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Physical
Xiaoqiang Fan, Xun Wang, Han Yan, Meng Cai, Wensheng Zhong, Hao Li, Minhao Zhu
Summary: This study introduces waterborne fluorinated polyacrylate (F-PA) complex latex particles into waterborne epoxy resin (EP) coatings to improve the coating's hydrophobicity, toughness, and corrosion resistance. The interpenetrating network polymer structure successfully solves the compatibility issue between F-PA and EP, resulting in enhanced mechanical and damping properties of the composite coating.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2022)
Article
Chemistry, Physical
Thitiya Boonma, Bodee Nutho, Bunleu Sungthong, Ployvadee Sripadung, Thanyada Rungrotmongkol, Nadtanet Nunthaboot
Summary: The atomistic molecular dynamics simulation shows that scandenin tends to form inclusion complexes with different types of cyclodextrin, with some cyclodextrins exhibiting higher inclusivity than others. The calculations indicate that modified cyclodextrins have a stronger binding affinity to scandenin compared to the parent host molecule.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Biochemistry & Molecular Biology
L. Paul, D. M. Shadrack, C. N. Mudogo, K. M. Mtei, R. L. Machunda, F. Ntie-Kang
Summary: The three-dimensional structure of cassava linamarase was established for the first time in this study using homology modeling, with molecular docking calculations and molecular dynamics simulations revealing its interaction with linamarin. The study sheds light on exploration of the enzyme's reaction mechanisms and provides insights into its stability through different computational approaches.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Polymer Science
Dongdong Li, Lukun Feng, Yin Tang, Caizhen Zhu
Summary: Tassieri et al. have introduced a novel rheological tool called i-Rheo GT that allows the evaluation of materials' linear viscoelastic properties from the relaxation modulus G(t) derived from molecular dynamics simulations. They estimated the polymers' entanglement characteristic time (tau e) from the crossover point of the moduli at intermediate times. The findings suggest that consistent values of tau e can be achieved by discarding the initial values of G(t) governed by bond-oscillation dynamics, and the effectiveness of i-Rheo GT is confirmed by different molecular dynamics simulations.
Article
Chemistry, Multidisciplinary
Gehui Zhang, Lingxin Lin, Wenhao Shen, Xue Wang, Yugang Wang, Liuxuan Cao, Feng Liu
Summary: A new strategy for high selectivity separation of alkali metal ions using artificial nanostructures has been reported in this study. The selectivity of ionic transport was found to reverse under pressure driving compared to electric field driving. Molecular dynamics simulations showed that different monovalent cations can be separated with unprecedentedly high selectivity by applying opposite-oriented pressure and electric fields.
Article
Chemistry, Physical
Xiuying Zhao, Yun Nie, Haoxiang Li, Haoyu Wu, Yangyang Gao, Liqun Zhang
Summary: The research explored the percolated network formed by mixed NPs of different sizes through molecular dynamics simulations, showing that big NPs are less conducive to building the network compared to small NPs. The analysis of dispersion state, cluster number, and size helps explain the percolation threshold during network formation. Shear flow leads to more contact aggregation structure of NPs, especially benefiting the formation of new percolated networks.
Article
Chemistry, Physical
Ye-Guang Fang, Xiaojiao Li, Yurui Gao, Yan-Hong Cui, Joseph S. S. Francisco, Chongqin Zhu, Wei-Hai Fang
Summary: We present an efficient method based on an extension of metadynamics for exploring complex free energy landscapes. The method greatly improves the performance of the metadynamics approach and allows for efficient modeling of chemical systems with complex free energy landscapes.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemical Research Methods
Indrani Baruah, Gargi Borgohain
Summary: This study investigates the effect of NADES on the stability of the protein beta-Lactoglobulin (BLG) at different temperatures using molecular dynamics simulations. It is found that NADES provides better stability to the protein up to a temperature of 400 K, but above this temperature, NADES fails to exert a stabilizing effect on the protein.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Article
Medicine, Research & Experimental
Aleksei Kabedev, Xuezhi Zhuo, Donglei Leng, Vito Fodera, Min Zhao, Per Larsson, Christel A. S. Bergstrom, Korbinian Lobmann
Summary: This study investigates the impact of drug loading on the stability of protein-stabilized amorphous formulations, finding a second glass transition temperature at drug loadings higher than 40-50%. The simulations suggest that the mechanisms of drug stabilization by proteins involve reduced mobility of drug molecules in the first drug shell and hydrogen-bond networks.
MOLECULAR PHARMACEUTICS
(2022)
Article
Biochemistry & Molecular Biology
Monica L. Fernandez-Quintero, Eugene F. DeRose, Scott A. Gabel, Geoffrey A. Mueller, Klaus R. Liedl
Summary: In this study, the conformational diversity of an anti-GFP-binding nanobody was characterized using molecular dynamics simulations and experimental data from NMR spectroscopy. The results showed excellent agreement between the distance maps obtained from NMR and MD simulations, as well as similar conformational spaces for simulations with and without time-averaged restraints. The motions observed in the ps-ns timescale, particularly in the CDR3 loop, also showed good agreement between measured and calculated order parameters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Franz Waibl, Johannes Kraml, Valentin J. Hoerschinger, Florian Hofer, Anna S. Kamenik, Monica L. Fernandez-Quintero, Klaus R. Liedl
Summary: This study extends the Grid Inhomogeneous Solvation Theory (GIST) algorithm to all solvents that can be modeled as rigid molecules. The method is validated through comparisons with thermodynamic integration (TI) calculations and experimental results, showing its reliability for different solvents. Additionally, the convergence of GIST in different solvents is investigated, and the study extends the applicability of the method.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Physiology
Yousra El Ghaleb, Nadine J. Ortner, Wilfried Posch, Monica L. Fernandez-Quintero, Wietske E. Tuinte, Stefania Monteleone, Henning J. Draheim, Klaus R. Liedl, Doris Wilflingseder, Joerg Striessnig, Petronel Tuluc, Bernhard E. Flucher, Marta Campiglio
Summary: This study reveals multiple regulatory mechanisms of the Ca(v)1.1 channel and the role of the gamma(1) subunit in its modulation. The inclusion of exon 29 in Ca(v)1.1a leads to reduced current density, which is further decreased by the presence of the gamma(1) subunit, inhibiting its activation. Additionally, the study suggests that the structural rearrangements induced by the inclusion of exon 29 may be crucial for the inhibitory action of the gamma(1) subunit.
JOURNAL OF GENERAL PHYSIOLOGY
(2022)
Article
Chemistry, Physical
Dennis F. Dinu, Pit Bartl, Patrick K. Quoika, Maren Podewitz, Klaus R. Liedl, Hinrich Grothe, Thomas Loerting
Summary: This study investigates the matrix-isolation infrared spectroscopy of CO2 monomers and dimers trapped in neon and air. Additional infrared-active bands are identified in the spectra due to the (CO2)2 dimer. The dimer is found to significantly increase the IR absorbance, suggesting its high fraction in the matrix experiments. The results improve understanding of the greenhouse effect for planets with thick CO2 atmospheres and highlight the importance of including dimer absorption in radiative forcing modeling databases.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Correction
Chemistry, Physical
Maren Podewitz, Yin Wang, Paraskevi Gkeka, Susanne von Grafenstein, Klaus R. Liedl, Zoe Cournia
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Inorganic & Nuclear
Reinhard Thaler, Holger Kopacka, Klaus Wurst, Thomas Mueller, Dennis F. Dinu, Klaus R. Liedl, Florian R. Neururer, Stephan Hohloch, Benno Bildstein
Summary: This article reports on the synthesis and properties of boron-substituted tromancenium salts, revealing their potential for novel synthetic applications.
Correction
Biochemistry & Molecular Biology
Monica L. Fernandez-Quintero, Patrick K. Quoika, Florian S. Wedl, Clarissa A. Seidler, Katharina B. Kroell, Johannes R. Loeffler, Nancy D. Pomarici, Valentin J. Hoerschinger, Alexander Bujotzek, Guy Georges, Hubert Kettenberger, Klaus R. Liedl
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Ferenc Torok, Kamer Tezcan, Ludovica Filippini, Monica L. Fernandez-Quintero, Lucia Zanetti, Klaus R. Liedl, Raphaela S. Drexel, Joerg Striessnig, Nadine J. Ortner
Summary: Germline gain-of-function missense variants in the CACNA1D gene can cause severe neurodevelopmental disorders with or without endocrine symptoms. We report a 4-week-old newborn with a novel de novo missense variant F747S in the Cav1.3 alpha 1-subunit, which is associated with a prominent jittering phenotype, developmental delay, elevated aldosterone level, and transient hypoglycemia. Functional experiments confirmed the pathogenicity of the variant and revealed significant changes in channel gating. The increased sensitivity to the L-type Ca2+ channel blocker isradipine suggests its potential as a treatment option for carriers of this mutation.
HUMAN MOLECULAR GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Rafael Eduardo Oliveira Rocha, Diego Cesar Batista Mariano, Tiago Silva Almeida, Leon Sulfierry CorreaCosta, Pedro Henrique Camargo Fischer, Lucianna Helene Santos, Ernesto Raul Caffarena, Carlos Henrique da Silveira, Leonida M. Lamp, Monica Lisa Fernandez-Quintero, Klaus Roman Liedl, Raquel Cardoso De Melo-Minardi, Leonardo Henrique Franca de Lima
Summary: In this study, the molecular basis of the thermostabilization of the Paenibacillus polymyxa GH1 beta-glucosidase by two-point mutations was investigated through molecular dynamics simulations and computational analyses. Three classic mechanisms were found to contribute to the stabilization of the thermostable mutants.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Chemistry, Medicinal
Sven Thamm, Marina K. Willwacher, Gary E. Aspnes, Tom Bretschneider, Nicholas F. Brown, Silke Buschbom-Helmke, Thomas Veser, Emanuele M. Gargano, Daniel Grabowski, Christoph Hoenke, Damian Matera, Katja Mueck, Stefan Peters, Sophia Reindl, Doris Riether, Matthias Schmid, Christofer S. Tautermann, Aaron M. Teitelbaum, Cornelius Truenkle, Martin Winter, Thomas Fox, Lars Wortmann
Summary: Genome-wide association studies have identified HSD17B13 as a potential target for the treatment of liver diseases, but its physiological function and disease-relevant substrate are unknown. In this study, a novel potent and selective HSD17B13 inhibitor (BI-3231) was identified through high-throughput screening using estradiol as a substrate. The compound was characterized for its functional, physicochemical, and DMPK properties, and its NAD+ dependency was investigated. To promote Open Science, the chemical probe BI-3231 will be made available to the scientific community for free.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Clarissa A. Seidler, Janik Kokot, Monica L. Fernandez-Quintero, Klaus R. Liedl
Summary: In this study, the conformational diversity of four VHH variants and their binding to hen egg-white lysozyme (HEL) were investigated. It was found that with an increase in affinity, the stability of the VHH structure increased and the residues contributing to antigen binding underwent significant changes. In addition, it was observed that the investigated nanobodies followed the conformational selection paradigm, with the binding competent conformation pre-existing within the structural ensembles without the presence of the antigen.
Article
Biochemistry & Molecular Biology
Nancy D. Pomarici, Roberta Cacciato, Janik Kokot, Monica L. Fernandez-Quintero, Klaus R. Liedl
Summary: This study investigates the evolution of immunoglobulin isotypes, highlighting the preserved features and the parts that have mutated over time. Coupled residues in the evolution process are crucial for maintaining the immunoglobulin fold and interactions with other domains. By comparing biophysical properties across different animal classes and isotypes, conserved residues in evolution can be identified. This study offers a general overview of the evolution of immunoglobulin isotypes and advances the understanding of their characteristic biophysical properties for guiding protein design.
Article
Food Science & Technology
Ricarda Zeindl, Annika L. Franzmann, Monica L. Fernandez-Quintero, Clarissa A. Seidler, Valentin J. Hoerschinger, Klaus R. Liedl, Martin Tollinger
Summary: Allergies related to kiwi consumption are on the rise, with cross-reactivity with birch pollen being a major factor. This study determined the three-dimensional structures of PR-10 proteins in kiwi fruits and found that they closely resemble the major allergen in birch pollen. Structural differences were observed compared to another kiwi allergen, Act d 11. Additionally, the study identified the presence of phenolic compound pyrogallol in kiwi proteins.
Article
Allergy
Florian Hofer, Anna-Lena Fischer, Anna S. Kamenik, Franz Waibl, Monica L. Fernandez-Quintero, Klaus R. Liedl
Summary: The profilin allergen family is a class of proteins that are found in plants, viruses, and various eukaryotes. They have a conserved structural fold but exhibit differences in their biophysical properties. In this study, molecular dynamics simulations were performed to investigate the functional differences of three profilin allergens. It was found that these differences are related to conformational flexibility and thermal stability, emphasizing the importance of flexibility in understanding the biophysical differences between structurally similar allergens.
FRONTIERS IN ALLERGY
(2022)
Meeting Abstract
Biophysics
Martin C. Heiss, Monica L. Fernandez-Quintero, Yousra El Ghaleb, Simone Pelizzari, Petronel Tuluc, Marta Campiglio, Klaus R. Liedl, Bernhard E. Flucher
BIOPHYSICAL JOURNAL
(2022)
