Article
Multidisciplinary Sciences
Oliver T. Unke, Stefan Chmiela, Michael Gastegger, Kristof T. Schuett, Huziel E. Sauceda, Klaus-Robert Mueller
Summary: SpookyNet is a deep neural network that addresses the issue of electronic degrees of freedom and nonlocality typically ignored in machine-learned force fields. By incorporating chemically meaningful inductive biases and analytical corrections into the network architecture, SpookyNet can improve performance in quantum chemistry and fill important gaps in machine learning models.
NATURE COMMUNICATIONS
(2021)
Article
Physics, Applied
Chunyu Li, Alejandro Strachan
Summary: Molecular dynamics simulations were used to study the shock-induced collapse of porosity and temperature distribution in 1,3,5,7-tetranitro-1,3,5,7-tetrazoctane. The study found that pore size and shape play a crucial role in the collapse mechanism and resulting temperature. The findings provide valuable information for predictive modeling of shock-induced initiation.
JOURNAL OF APPLIED PHYSICS
(2022)
Article
Biophysics
Yuliang Sun, Zhixiong Deng, Xukai Jiang, Bing Yuan, Kai Yang
Summary: The study revealed that PMB has a preference for specific lipid species in its interaction with different membrane systems, leading to complex membrane interaction states. These findings provide insights into the action mechanism of PMB at a membrane level, laying the foundation for developing novel and safer polymyxin strategies for better clinical use.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2022)
Article
Biophysics
Federico Sebastiani, Hanna Michlits, Bettina Lier, Maurizio Becucci, Paul G. Furtmueller, Chris Oostenbrink, Christian Obinger, Stefan Hofbauer, Giulietta Smulevich
Summary: This study focused on the actinobacterial ChdC from Corynebacterium diphtheriae to elucidate the hydrogen peroxide-mediated reaction mechanism and the impact of protein mutations on reaction intermediates. The experimental results showed that specific mutations could affect the generation of reaction products, further revealing the importance of MMD in the reaction process.
BIOPHYSICAL JOURNAL
(2021)
Article
Polymer Science
Peiyuan Gao, Scott E. Muller, Jaehun Chun, Lirong Zhong, Zachary C. Kennedy
Summary: This study investigates the relationship between the rheological properties and the structure of a polymer-2D filler system by experiment and simulation methods. The effects of filler size, filler content, surface chemistry, and shear rate on a high-performance polymer (PEKK) with 2D filler (mica) composite are systematically studied. The results show that the interaction between the polymer and 2D filler has two different consequences on tuning the viscosity of the composite.
Article
Chemistry, Physical
Giacomo Buccella, Andrea Villa, Davide Ceresoli, Luca Barbieri, Roberto Malgesini, Andres R. Leon-Garzon
Summary: This study compares two different models for the deterioration process of polyethylene exposed to reactive plasma. The first model successfully reproduces the experimentally detected oxidation of the polyethylene surface, while the second model explains the presence of nitrogen on the sample surface.
APPLIED SURFACE SCIENCE
(2021)
Article
Chemistry, Physical
Derek S. Wang, Tomas Neuman, Susanne F. Yelin, Johannes Flick
Summary: This study explores the influence of an optical cavity on intramolecular vibrational energy redistribution and demonstrates that optical cavity resonance coupling can alter the rates of unimolecular dissociation reactions.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Maksim Kulichenko, Justin S. Smith, Benjamin Nebgen, Ying Wai Li, Nikita Fedik, Alexander Boldyrev, Nicholas Lubbers, Kipton Barros, Sergei Tretiak
Summary: Machine learning is rapidly becoming a key tool for modeling chemical processes and materials, especially with the development of ML-based force fields for interatomic potentials. Designing high-quality training data sets is crucial for model accuracy, with strategies like active learning and using high levels of quantum theory to enhance training. Transfer learning allows for training on mixed fidelity data sets, showing significant improvements in model accuracy.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Multidisciplinary Sciences
N. Gao, Z. W. Yao, G. H. Lu, H. Q. Deng, F. Gao
Summary: The study found a new diffusion mechanism for <100> interstitial dislocation loops in BCC iron using self-adaptive accelerated molecular dynamics, which represents a significant step towards understanding the mechanical behavior and microstructure evolution of the material.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Zhaleh Ghaemi, Martin Gruebele, Emad Tajkhorshid
Summary: The disassembly process of HBV capsid involves structurally heterogeneous cracks mainly within hexameric sites, with only a small subset of capsid protein monomers engaged in each instance of disassembly. Specific residues at interfaces between dimers within hexamers, such as R127, I139, Y132, N136, A137, and V149, are identified as hot spots for disassembly by avoiding overstabilization of capsids, and are evolutionarily conserved.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Punam Rattu, Bastien Belzunces, Taylor Haynes, Chris-Kriton Skylaris, Syma Khalid
Summary: The study investigates the impact of nanopores with hydrophobic constrictions on DNA translocation, finding that aromatic residues slow down the process. Stressed DNA strands exhibit greater variability in translocation rates, and the number of DNA entries into the pores correlates with pore width.
Review
Chemistry, Physical
Outi Haapanen, Vivek Sharma
Summary: Respiratory complex I plays a crucial role in the electron transport chains of mitochondria and bacteria by efficiently coupling the redox reaction and proton pumping through a unique tunnel, leading to the synthesis of ATP. The separation of redox reaction and proton pumping in space and time raises the question of how these two reactions are so efficiently coupled. Recent structural data and molecular simulations provide insights into how quinone reduction and dynamics may be linked to proton pumping in complex I.
CURRENT OPINION IN ELECTROCHEMISTRY
(2021)
Article
Mechanics
Xin-Xin Wang, Jian-Li Shao, Bao Wu, Sheng-Ning Yan, An-Min He, Pei Wang
Summary: Using molecular dynamics, this study investigated the impact of nanoscale helium bubbles on the formation of micro-jets under supported and unsupported shock wave loading. The simulations reveal that the local dynamics of the nano-He bubbles primarily influence the micro-jet formation. The expansion of the He bubbles accelerates the velocity of the jet head but this effect disappears during the tensile stage.
Article
Chemistry, Physical
Robert G. Alberstein, Jesse L. Prelesnik, Elias Nakouzi, Shuai Zhang, James J. De Yoreo, Jim Pfaendtner, F. Akif Tezcan, Christopher J. Mundy
Summary: Understanding templated molecular assembly on solid surfaces requires understanding the aqueous response to the surface under different solution conditions. In this study, we investigate the molecular-scale response to different mica surfaces and identify distinct solvent orientations that create directional potentials for macromolecule adsorption. We correlate this directionality with the epitaxial alignment of designed proteins on the surfaces and confirm our findings through atomic force microscopy experiments. Our work provides insights into the electrolyte response near mineral interfaces and highlights the role of solvent in predicting hierarchical material assembly on mineral surfaces.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
D. Aristoff, J. Copperman, G. Simpson, R. J. Webber, D. M. Zuckerman
Summary: The weighted ensemble (WE) method, an enhanced sampling approach, has gained popularity in computational biochemistry due to improved hardware, software, and algorithmic advancements. Recent results have led to greater computational efficiency, particularly through variance reduction approaches for managing trajectories in systems of any dimensionality.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Giulia Di Rocco, Fabrizio Bernini, Gianantonio Battistuzzi, Antonio Ranieri, Carlo Augusto Bortolotti, Marco Borsari, Marco Sola
Summary: In this study, it was found that human neuroglobin (hNgb) undergoes H2O2-induced breakdown of the heme center at a slower rate than other globins. The rate is affected by the Cys46/Cys55 disulfide bond and the non-covalent interactions involving Tyr44, Lys67, the His64 heme iron axial ligand, and the heme propionate-7. The presence of a disulfide bridge, as well as certain mutations, can influence the rate and formation of beta-amyloid aggregates.
Article
Biochemistry & Molecular Biology
Daniel Schmidt, Nikolaus Falb, Ilenia Serra, Marzia Bellei, Vera Pfanzagl, Stefan Hofbauer, Sabine Van Doorslaer, Gianantonio Battistuzzi, Paul G. Furtmuller, Christian Obinger
Article
Chemistry, Medicinal
Oriol Gracia Carmona, Chris Oostenbrink
Summary: One of the most challenging aspects in the molecular simulation of proteins is studying the slowly relaxing processes. State-of-the-art methods rely on performing several short simulations, but capturing these processes is difficult. A recently developed technique called accelerated enveloping distribution sampling (AEDS) can overcome the high-energy-barrier challenge and sample the relevant degrees of freedom accurately. In this study, AEDS is applied to the T4 lysozyme L99A system, showcasing its advantages and challenges. The results demonstrate the potential of AEDS in responding to more intricate molecular events.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Andrea Dali, Thomas Gabler, Federico Sebastiani, Alina Destinger, Paul Georg Furtmueller, Vera Pfanzagl, Maurizio Becucci, Giulietta Smulevich, Stefan Hofbauer
Summary: Coproporphyrin ferrochelatases (CpfCs) are enzymes that catalyze the penultimate step in the coproporphyrin-dependent heme biosynthesis pathway. The discovery of the correct substrate for these ferrochelatases and the characterization of their binding mode provide valuable insights into the iron insertion process. This knowledge is essential for understanding the preconditions and mechanisms of iron insertion in CpfCs.
Article
Biochemistry & Molecular Biology
Federico Sebastiani, Chiara Baroni, Gaurav Patil, Andrea Dali, Maurizio Becucci, Stefan Hofbauer, Giulietta Smulevich
Summary: Monoderm bacteria accumulate heme b through the coproporphyrin-dependent biosynthesis pathway. The decarboxylation of propionate groups in coproheme by coproheme decarboxylase (ChdC) is a stepwise process. H-bond interactions in the pocket of ChdCs play a crucial role in stabilizing the active site and enzyme functionality, which were evaluated through characterization of mutants complexed with coproheme and heme b via spectroscopies.
Article
Biochemistry & Molecular Biology
Daniel R. Ramos, Paul G. Furtmueller, Christian Obinger, Angeles Pena-Gallego, Ignacio Perez-Juste, J. Arturo Santaballa
Summary: Electronic structure calculations using DFT were conducted to examine the influence of water molecules and protonation on the heme group of peroxidases in different redox and spin states. The study discusses shared geometries, spectroscopic properties, and thermodynamics of peroxidases. Computed Gibbs free energies suggest that the corresponding aquo complexes are not thermodynamically stable, supporting the five-coordinate Fe(III) center in native ferric peroxidases with a non-bonding water molecule. Protonation of the ferryl oxygen of compound II is found to be necessary and computed Gibbs free energies reveal pK(a) values of approximately 8.5-9.0 for compound II.
Article
Cell Biology
Sophie Broadway-Stringer, He Jiang, Kirsty Wadmore, Charlotte Hooper, Gillian Douglas, Violetta Steeples, Amar J. Azad, Evie Singer, Jasmeet S. Reyat, Frantisek Galatik, Elisabeth Ehler, Pauline Bennett, Jacinta I. Kalisch-Smith, Duncan B. Sparrow, Benjamin Davies, Kristina Djinovic-Carugo, Mathias Gautel, Hugh Watkins, Katja Gehmlich
Summary: Pathogenic variants in ACTN2 gene have been identified as rare causes of Hypertrophic Cardiomyopathy. However, the underlying disease mechanisms are not well understood. This study found that a missense variant in alpha-actinin renders the protein less stable, leading to molecular and morphological abnormalities in mouse hearts.
Article
Agronomy
Yerko Escalona, Drazen Petrov, Edgar Galicia-Andres, Chris Oostenbrink
Summary: By using molecular dynamics simulations and creating molecular systems that resemble soil organic matter (SOM), researchers gained a better understanding of SOM. They studied standardized samples of humic substances (HSs) from various sources and analyzed the structure and dynamics to explore the relationship between properties and protonation state of carboxyl groups as well as the influence of ion interactions and pH.
Article
Biochemistry & Molecular Biology
Gaurav Patil, Hanna Michlits, Paul G. Furtmueller, Stefan Hofbauer
Summary: Coproheme decarboxylases (ChdCs) are enzymes involved in the biosynthesis of heme. This study focuses on the second part of the decarboxylation reaction catalyzed by ChdCs, which has not been previously studied. The researchers optimized the production and purification of a intermediate compound called monovinyl, monopropionate deuteroheme (MMD), and used it to study the reaction mechanism. The results indicate that the second part of the reaction is similar to the first part, with slight differences in the active site architecture and H-bonding network.
Article
Biochemistry & Molecular Biology
Federico Sebastiani, Andrea Dali, Diego Javier Alonso de Armino, Lorenzo Campagni, Gaurav Patil, Maurizio Becucci, Stefan Hofbauer, Dario A. Estrin, Giulietta Smulevich
Summary: This study focuses on the carbon monoxide adducts of the wild-type and selected variants of the coproheme decarboxylase from actinobacterial Corynebacterium diphtheriae complexed with coproheme, monovinyl monopropionyl deuteroheme (MMD), and heme b. The results show that the wild-type coproheme-CO adduct is characterized by two CO conformers, hydrogen-bonded and weak polar interaction with the distal cavity. The absence of the H118 residue leads to the formation of non-H-bonded CO species. In addition, CO binding to reversed heme b and heme d is also investigated in this work.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Thomas Gabler, Andrea Dali, Federico Sebastiani, Paul Georg Furtmueller, Maurizio Becucci, Stefan Hofbauer, Giulietta Smulevich
Summary: Understanding the reaction mechanism of enzymes is challenging, but studying model substrates can provide valuable information. In this study, we investigated the mechanism of ferrous iron incorporation in a bacterial enzyme complex and discovered the role of hydrogen bond interactions in this process.
Editorial Material
Biochemistry & Molecular Biology
Oliviero Carugo, Kristina Djinovic-Carugo
Summary: In the past 2 decades, structural biology has evolved from a single technique for individual proteins to a multimodal integrative approach. Recently, protein structure prediction algorithms have provided new possibilities for tackling challenging biological questions.
Review
Biochemistry & Molecular Biology
Nikolaus Falb, Gaurav Patil, Paul G. Furtmueller, Thomas Gabler, Stefan Hofbauer
Summary: The coproporphyrin dependent heme biosynthesis pathway is predominantly used by Gram-positive bacteria. This pathway is of interest for basic research as it relates to medical biotechnology and the development of new antibiotic targets against Gram-positive superbugs. A review of the accumulated structural data on the enzymes involved in this pathway is provided, highlighting the need for further analysis and future research to gain a comprehensive understanding of prokaryotic heme biosynthesis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Oriol Gracia Carmona, Majd Lahham, Peter Poliak, Dominic Goj, Eva Friesser, Silvia Wallner, Peter Macheroux, Chris Oostenbrink
Summary: This study investigates the substrate specificity of the FsqB enzyme and discovers the role of tyrosine and aspartate residues in fixing the substrate close to the isoalloxazine ring of the cofactor. The combination of experimental and theoretical approaches helps solve the mystery behind the activity of FsqB enzyme.
JOURNAL OF MOLECULAR RECOGNITION
(2023)