Article
Optics
Lewis W. Anderson, Martin Kiffner, Panagiotis Kl. Barkoutsos, Ivano Tavernelli, Jason Crain, Dieter Jaksch
Summary: The study develops a coarse-grained representation of electronic response suitable for determining the ground state of weakly interacting molecules using VQA, demonstrating its capability on IBM superconducting quantum processors and showing potential for probing energies in weakly bound regimes.
Article
Physics, Multidisciplinary
Xuegui Lin, Xiaojie Chen, Qing Liang
Summary: The study found that spectrins prefer to interact with phosphatidylethanolamine (PE) lipids, and tend to contact with the liquid-disordered (Ld) domains enriched in unsaturated PE. Anionic lipids enhance the attraction between spectrins and lipid domains, while residue mutation decreases the structural stability of spectrins.
Article
Engineering, Biomedical
Giuseppe Florio, Nicola M. Pugno, Markus J. Buehler, Giuseppe Puglisi
Summary: The study proposes a simple general framework to predict various aspects of protein structural analyses, focusing on global features of the proteins. The model is demonstrated to be effective in capturing the folding and unfolding behaviors of tropoelastin and its mutations. Additionally, the approach is shown to reproduce important properties of the folding-unfolding mechanical response.
ACTA BIOMATERIALIA
(2021)
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, Medicinal
Baocai Ma, Zuoheng Zhang, Yan Li, Xubo Lin, Ning Gu
Summary: Coarse-grained models allow for the investigation of simulation system dynamics on a larger scale and longer time scale, making them suitable for studying macromolecular systems. In this work, coarse-grained molecular dynamics simulations were performed to reveal the interaction details between SARS-CoV-2 RBD and ACE2. The results provide insights into the binding process and potential drug targets for combating SARS-CoV-2.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Jinyin Zha, Fei Xia
Summary: Simulating the conformations and functions of biological macromolecules using all-atom (AA) models is costly, but a possible solution is to develop hybrid AA/UCG models. In this study, we developed hybrid models and used them to investigate the conformational changes of microtubule-bound tubulins. Results showed the mechanism of selective binding of taxol molecules to microtubules. We also explored the interactions between microtubules and dyneins, demonstrating the potential of the hybrid AA/UCG model in studying complex biological systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Kazuhiko Honda
Summary: The procedure for generating coarse-grained potential based on liquid state simulations is applied to liquid methane. The spherically projected potential approach consistently generates the effective pair potential for liquid methane, and the difference between the potential profile and the potential of mean force reflects the many-body contribution to liquid structure.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Mechanics
Yann Dufresne, Micael Boulet, Stephane Moreau
Summary: CGDEM is a valuable option for large-scale industrial applications to reduce the cost of classic DEM computations. This study compares three solutions from the literature to overcome the reduction in collision frequency in CGDEM simulations. The results confirm the existence of an inverse law for the drop in collision frequency and suggest that CGDEM simulations may be more stable than regular DEM simulations.
Article
Chemistry, Physical
Srdjan Pusara, Peyman Yamin, Wolfgang Wenzel, Marjan Krstic, Mariana Kozlowska
Summary: Colloidal protein-protein interactions play a crucial role in biotechnological processes, but are complex and difficult to understand through measurements alone. The osmotic second virial coefficient, B-22, can be used to estimate these interactions in diluted protein solutions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Jaehyeok Jin, Gregory A. Voth
Summary: Systematic bottom-up coarse-graining is a useful approach for exploring different length and time scales in molecular systems. However, the configuration dependence of coarse-grained interactions limits their applicability. In this study, a statistical mechanical theory is proposed to design coarse-grained interactions across different configurations and conditions. By identifying classical coarse-grained free energy surfaces for characteristic configurations and quantifying the coupling interaction between them, the theory accurately captures the underlying potential of mean force in coarse-grained variables and offers a new protocol for multiscale model design.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Hiram Isaac Beltran, Salomon J. Alas-Guardado, Pedro Pablo Gonzalez-Perez
Summary: In this study, the folding of 7 hydrophobic-polar sequences in two types of 2D-square space lattices, homogeneous and correlated, was tested. It was found that using correlated networks led to more successful structural trials compared to a homogeneous lattice. The majority of the sequences were designed by the researchers, and the goal of the study was to obtain a modified 2D HP lattice model that mimics protein folding in crowded environments. The results showed that folding sequences in crowded spaces achieved better results than in homogeneous ones.
JOURNAL OF MOLECULAR MODELING
(2022)
Review
Physics, Multidisciplinary
Tanja Schilling
Summary: This article discusses the construction of coarse-grained models for systems out of thermal equilibrium, including both equilibrium and non-equilibrium coarse-graining methods and numerical schemes.
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS
(2022)
Article
Multidisciplinary Sciences
Aya Okuda, Masahiro Shimizu, Ken Morishima, Rintaro Inoue, Nobuhiro Sato, Reiko Urade, Masaaki Sugiyama
Summary: Multi-domain proteins exhibit various domain conformations under physiological conditions to regulate their functions through conformational changes. ER-60, a typical MDP protein folding enzyme, is found to have different domain conformations in solution depending on the redox state, with oxidized and reduced ER-60 structures differing from each other. Structural modeling with coarse-grained molecular dynamics simulation indicates that the distance between the two edge domains of oxidized ER-60 is longer and one edge domain has a more flexible conformation compared to reduced ER-60.
SCIENTIFIC REPORTS
(2021)
Article
Physics, Fluids & Plasmas
M. Reza Parsa, Changho Kim, Alexander J. Wagner
Summary: In this study, the authors discuss the issue of momentum definition in coarse-grained descriptions of microscopic systems, particularly the discrepancy between the fluctuating properties of common momentum definitions in lattice gas and lattice Boltzmann methods and a fundamental definition of momentum. Analytical representations for the distribution of different momentum measures are derived, providing a comprehensive account of these differences.
Article
Chemistry, Physical
Saientan Bag, Melissa K. Meinel, Florian Mueller-Plathe
Summary: In this paper, a data-driven approach to generate coarse-grained models that preserve the all-atom molecular mobility is presented. The researchers designed an artificial neural network model that can predict the simulation-ready coarse-grained potential based on the input of all-atom force field parameters. Experimental results showed that the predicted coarse-grained potential can significantly reduce the artificial acceleration in molecular mobility, making the coarse-grained models more accurate.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Mareike Wiedmann, Patricia K. Dranchak, Mahesh Aitha, Bryan Queme, Christopher D. Collmus, Maithri M. Kashipathy, Liza Kanter, Laurence Lamy, Joseph M. Rogers, Dingyin Tao, Kevin P. Battaile, Ganesha Rai, Scott Lovell, Hiroaki Suga, James Inglese
Summary: A detailed structure-activity relationship of the iPGM inhibitor ipglycermide was constructed using 280 substituted analogs, revealing the high affinity binding and freeze of iPGMs into inactive, stable complexes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Carmen Suay-Corredera, Maria Rosaria Pricolo, Diana Velazquez-Carreras, Divya Pathak, Neha Nandwani, Carolina Pimenta-Lopes, David Sanchez-Ortiz, Inigo Urrutia-Irazabal, Silvia Vilches, Fernando Dominguez, Giulia Frisso, Lorenzo Monserrat, Pablo Garcia-Pavia, David de Sancho, James A. Spudich, Kathleen M. Ruppel, Elias Herrero-Galan, Jorge Alegre-Cebollada
Summary: Hypertrophic cardiomyopathy (HCM) is a disease caused by mutations in sarcomeric proteins, with many mutations not affecting protein structure or stability. Research shows that these mutations may disrupt the nanomechanics of cMyBP-C, affecting its regulatory role in actomyosin filaments.
Article
Chemistry, Physical
Ion Mitxelena, Xabier Lopez, David de Sancho
Summary: Markov state models (MSMs) are a preferred method for analyzing and interpreting molecular dynamics simulations of conformational transitions in biopolymers. By utilizing hierarchical density-based clustering, it is possible to define slow dynamics more effectively and consistently with the assumption of Markovianity.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Applied
Apostolos A. Sevastos, Christopher M. Baker, Philip Taylor
Summary: This study presents a simple method for calculating logP(alk) for nonionic surfactants at sub-micellar concentrations by using a linear combination of octanol/water partition and hydrogen-bonding contribution parameters. The model incorporates a critical folding chain length factor to address entropic effects from ethylene-oxide chain conformational behavior for alcohol ethoxylate surfactants, which was validated through molecular dynamics simulations. The model outperforms previously published methods and can be applied in surfactant research and regulatory submissions without experimental data.
JOURNAL OF SURFACTANTS AND DETERGENTS
(2022)
Article
Chemistry, Physical
Christina Felbek, Federica Arrigoni, David de Sancho, Aurore Jacq-Bailly, Robert B. Best, Vincent Fourmond, Luca Bertini, Christophe Leger
Summary: The study investigates the inhibitory mechanism of hydrogen sulfide on FeFe hydrogenase through a combination of various experimental and theoretical methods, revealing the underlying mechanisms and providing insights into the oxidation and reduction of the enzyme. Additionally, it was observed that the inhibition by sulfide may lead to irreversible inactivation of the hydrogenase.
Article
Chemistry, Multidisciplinary
Nicole Y. Meredith, Stefan Borsley, Ivan Smolyar, Gary S. Nichol, Christopher M. Baker, Kenneth B. Ling, Scott L. Cockroft
Summary: This study used synthetic molecular balances to quantify the energetics of amine/amide H-bonds in different solvents, effectively isolating the typically dominant influence of the solvent. The correlations between experimental and computed energies were found to vary depending on the solvent, but excellent correlations were achieved after dissecting solvent effects using Hunter's solvation model. Changes in the fitted constants revealed the energetics of secondary local interactions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Physical
Asier Urriolabeitia, David De Sancho, Xabier Lopez
Summary: In this study, computer simulations were used to investigate the influence of mimosine on peptide structure. The results showed that the dipole nature of mimosine leads to a preference for stacked conformations. Quantum mechanical calculations were employed to validate the results.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Jesper E. Dreier, Andreas Prestel, Joao M. Martins, Sebastian S. Brondum, Olaf Nielsen, Anna E. Garbers, Hiroaki Suga, Wouter Boomsma, Joseph M. Rogers, Rasmus Hartmann-Petersen, Birthe B. Kragelund
Summary: A disordered ubiquitin-binding motif (DisUBM) has been discovered, which can remain disordered when bound and has functions in degradation and transcription. The motif relies on aromatic and negatively charged residues, has low and moldable affinity, and can increase the interaction surface with ubiquitin. DisUBMs can emerge from unbiased screening of randomized peptide libraries.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biophysics
David De Sancho
Summary: Macromolecular phase separation plays a crucial role in the formation of membraneless organelles and cellular organization. The formation of condensate-spanning networks in protein solutions is determined by the interplay between two classes of residues, stickers and spacers, with multivalency and sequence patterning being the main determinants for phase separation. Atomistic molecular dynamics simulations demonstrate that ternary amino acid mixtures involving both sticker and spacer types can undergo phase separation, resulting in phases with intermediate compaction and greater fluidity compared to sticker-only condensates.
BIOPHYSICAL JOURNAL
(2022)
Article
Physics, Multidisciplinary
Antonio Reifs, Irene Ruiz Ortiz, Amaia Ochandorena Saa, Jorg Schonfelder, David De Sancho, Victor Munoz, Raul Perez-Jimenez
Summary: Ultrafast folding proteins have low energetic barriers and fast kinetics, making them suitable for study by both experiments and simulations. However, single molecule force spectroscopy experiments on these proteins are challenging due to the lack of mechanical fingerprints. In this study, the unfolding of an ultrafast protein is investigated using atomic force microscopy experiments.
COMMUNICATIONS PHYSICS
(2023)
Article
Agronomy
Maddalena Bronzato, Adam Burriss, Nikita King, Claire Donaldson, Danielle Sayer, Christopher M. Baker
Summary: Photostability is an important property in agrochemicals, and the traditional measurement method neglects factors that influence photostability under field conditions. The new assay using leaf tissue as a substrate provides more accurate results. It can measure the interaction between photodegradation and foliar uptake under standardized laboratory conditions.
PEST MANAGEMENT SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Julie E. Bolding, Alexander L. Nielsen, Iben Jensen, Tobias N. Hansen, Line A. Ryberg, Samuel T. Jameson, Pernille Harris, Guenther H. J. Peters, John M. Denu, Joseph M. Rogers, Christian A. Olsen
Summary: Sirtuins are a group of proteins that play important roles in regulating gene expression and metabolism in humans. Among the seven isoforms, SIRT7 has been less studied, but this study reveals its specific functions in the nucleus and nucleolus, as well as compounds that modulate its activity.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
David Silva-Brea, David de Sancho, Xabier Lopez
Summary: Quantum mechanical calculations are used to understand the preferred modes of chelation in metal-binding peptides and determine binding affinities. While increasing coordination of a metal leads to higher stabilization energies, it also results in reduced conformational freedom of the polypeptide chain and a penalty in entropy. The negative correlation between stabilization energy and entropy suggests a delicate interplay between enthalpic and entropic forces in determining the most favorable species, and this finding has implications for the Metal Ion Hypothesis.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Asier Urriolabeitia, David De Sancho, Xabier Lopez
Summary: This study investigates the influence of the nonprotein amino acid mimosine on peptide structure using computer simulations. The results show that mimosine prefers a stacked conformation of the amino acid rings. Quantum mechanical calculations validate the findings of the simulations.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Joseph M. Rogers, Mickal Nawatha, Betsegaw Lemma, Ganga B. Vamisetti, Ido Livneh, Uri Barash, Israel Vlodavsky, Aaron Ciechanover, David Fushman, Hiroaki Suga, Ashraf Brik
Summary: A recent discovery of small, non-proteinogenic cyclic peptides capable of binding specific Ub chains has shown promising anti-cancer activity in vivo. This highlights the potential of non-proteinogenic cyclic peptide screening in rapidly identifying in vivo-active leads for targeting ubiquitin chains as an anti-cancer mechanism of action.
RSC CHEMICAL BIOLOGY
(2021)