Article
Biochemical Research Methods
Martin Kern, Sabrina Jaeger-Honz, Falk Schreiber, Bjorn Sommer
Summary: Molecular dynamics simulations provide insights into complex processes in cell membranes, and APL@Voro is a software that allows for interactive visualization and analysis of these simulations. It offers newly implemented algorithms and features to explore cell membrane compositions and dynamics.
Article
Chemistry, Physical
Majid Jafari, Faramarz Mehrnejad, Reza Talandashti, Farahnoosh Doustdar, Mohammad Reza Vakili, Afsaneh Lavasanifar
Summary: This study simulated 15 molecular systems to characterize the interactions between PAMAM dendrimers and membranes with different cholesterol ratios, explaining the structural features and geometry of their activity against cancer cells. The results demonstrated that cholesterol content in the membranes influenced the local membrane order parameters, and the dendrimers were able to create holes in cholesterol-containing membranes through hydrogen bonds and electrostatic interactions. Additionally, negatively charged phospholipids in cancer cell membranes played a crucial role in binding with the dendrimers, providing mechanistic insight into their activity against cancer cells.
APPLIED SURFACE SCIENCE
(2021)
Article
Chemistry, Medicinal
Barbara Mavroidi, Archontia Kaminari, Elias Sakellis, Zili Sideratou, Dimitris Tsiourvas
Summary: This study investigated the effect of carbon dots on a model cell membrane. The results showed that carbon dots interact with liposomes, affecting the structure and thermodynamic properties of the bilayer. Furthermore, carbon dots increased the membrane's permeability to the anticancer drug doxorubicin.
Article
Chemistry, Physical
Fikret Aydin, Aleksander E. P. Durumeric, Gabriel C. A. da Hora, John D. M. Nguyen, Myong In Oh, Jessica M. J. Swanson
Summary: This study investigates the permeation mechanism of a drug molecule through a multicomponent membrane using molecular dynamics simulations and transition-tempered metadynamics. The use of collective variables obtained from an unsupervised machine learning algorithm improves performance and accelerates convergence of permeation potential calculations. The addition of cholesterol to the lipid bilayer increases the width and height of the free energy barrier, while also affecting the resistance to permeation in the lipid head group region.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Ji Min Baek, Woo Hyuk Jung, Eui-Sang Yu, Dong June Ahn, Yong -Sang Ryu
Summary: Passive water penetration across the cell membrane is essential for cell volume homeostasis. By studying cholesterol-enriched lipid rafts, we confirmed the suppressed water permeation and the biological role of lipid composition in water translocation. Molecular dynamics simulations also demonstrated improved membrane stability under hypertonic conditions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Le Luo, Swathi Manda, Yunjeong Park, Busra Demir, Jesse Sanchez, M. P. Anantram, Ersin Emre Oren, Ashwin Gopinath, Marco Rolandi
Summary: This study presents the integration of DNA nanopores with bioprotonic contacts to create programmable and efficient artificial ion-channel interfaces. This robust interface allows for electronic recognition and quantification of biomolecular signals.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Daniel A. Olaya-Munoz, Juan P. Hernandez-Ortiz, Monica Olvera de la Cruz
Summary: Controlling the aggregation of dielectric particles can be achieved by adjusting their geometry and contact surface.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Food Science & Technology
Natalia Kuzmina, Pavel Volynsky, Ivan Boldyrev, Anna Alekseeva
Summary: Bee venom PLA2 exhibits two additional interface binding modes and enzyme activity through constant switching between different orientations. This switching has biological significance in terms of enzyme movement along the membrane, product release in a biological milieu, and enzyme desorption from the bilayer surface.
Article
Biochemistry & Molecular Biology
Vivien Walter, Celine Ruscher, Adrien Gola, Carlos M. Marques, Olivier Benzerara, Fabrice Thalmann
Summary: Atomistic molecular dynamics simulations have advanced to a level where they can investigate the lipid polymorphism of model bilayers at various temperatures, but may still struggle to accurately describe certain phases. Simulations on lipid bilayers of different sizes have shown that large systems may exhibit unexpected structural phases influenced by thermal history and preparation conditions. A mechanism for the observed topographic instability has been proposed.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2021)
Article
Chemistry, Physical
Shunta Kikuchi, Hiroshi Watanabe
Summary: We studied the effect of surfactants on the interface between two liquids using molecular dynamics simulation. Surfactants were represented by a simple bead-spring model with two atoms. By adjusting the bond length, we controlled the interfacial tension of the surfactant on the interface. The interface remained stable even at virtually zero interfacial tension, although its structure changed with different magnitudes of interfacial tension. The Fourier spectrum analysis showed a crossover from q(2) to q(4) when the interfacial tension approached zero, indicating that bending rigidity played a dominant role in the restoring force when surfactant molecules were sufficiently absorbed on the interface and the interfacial tension was close to zero, while interfacial tension dominated when it had finite values.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Isaac K. Asare, Alberto Perez Galende, Andres Bastidas Garcia, Mateo Fernandez Cruz, Anna Clara Miranda Moura, Conner C. Campbell, Matthew Scheyer, John Paul Alao, Steve Alston, Andrea N. Kravats, Charles R. Sanders, Gary A. Lorigan, Indra D. Sahu
Summary: This study examined the structural dynamics of KCNE3 in different lipid environments using molecular dynamics simulations. The results showed that the transmembrane domain of KCNE3 is more stable, while the N- and C-termini exhibit different levels of flexibility in various lipid conditions. The study also determined the specific locations of KCNE3 within the lipid membrane.
Article
Chemistry, Physical
Patrick G. Sahrmann, Timothy D. Loose, Aleksander E. P. Durumeric, Gregory A. Voth
Summary: In this work, a new method is proposed to improve the accuracy of coarse-grained (CG) models of biomolecules by incorporating virtual particles as latent variables. The virtual particle interactions are optimized through a gradient descent algorithm aided by machine learning, capturing solvent-mediated behavior and higher-order correlations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Paolo Marracino, Laura Caramazza, Maria Montagna, Ramin Ghahri, Marco D'Abramo, Micaela Liberti, Francesca Apollonio
Summary: Electroporation is a technique that enhances cell membrane permeability by inducing reversible membrane pores using an electric field. This study proposes a three-state kinetic model based on the mechanism of water defects intruding at the water/lipid interface under electric field intensities. The model, supported by robust statistical sampling, provides kinetic constants for transitions from an intact bilayer state to a hydrophobic pore state.
BIOELECTROCHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Maria Joao Moreno, Luis M. S. Loura, Jorge Martins, Armindo Salvador, Adrian Velazquez-Campoy
Summary: This review article discusses various methods and formalisms for analyzing the equilibrium distribution of ligands in the presence of proteins, lipid membranes, or both, with special attention to common pitfalls and validity limits of different approaches. The analysis of ligand binding through Stern-Volmer plots of protein fluorescence quenching is emphasized for its widespread use in characterizing interactions. Different systems of increasing complexity are considered, from proteins with single to multiple binding sites to membrane proteins in lipid bilayers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Albert A. Smith, Alexander Vogel, Oskar Engberg, Peter W. Hildebrand, Daniel Huster
Summary: Biomolecular function is based on a complex hierarchy of molecular motions. This study presents an approach to construct the dynamic landscape of biomolecules, which captures the aggregate influence of multiple motions acting on various timescales and positions.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Andrey A. Gurtovenko, Evgenii I. Mukhamadiarov, Andrei Yu. Kostritskii, Mikko Karttunen
JOURNAL OF PHYSICAL CHEMISTRY B
(2018)
Article
Chemistry, Physical
Andrey A. Gurtovenko, Matti Javanainen, Fabio Lolicato, Ilpo Vattulainen
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2019)
Article
Chemistry, Physical
Andrey A. Gurtovenko
JOURNAL OF PHYSICAL CHEMISTRY B
(2019)
Article
Chemistry, Multidisciplinary
Andrey A. Gurtovenko, Mikko Karttunen
Article
Thermodynamics
Victor M. Nazarychev, Artyom D. Glova, Igor V. Volgin, Sergey Larin, Alexey Lyulin, Sergey Lyulin, Andrey A. Gurtovenko
Summary: This study investigates the effects of different atomistic force field models on the calculation of thermal conductivity of n-eicosane samples using molecular dynamics simulations. The results show significant differences in the performance of different models in crystalline and liquid states, highlighting the challenging task of selecting an appropriate model for thermal conductivity calculations.
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
(2021)
Article
Chemistry, Physical
Artyom D. Glova, Victor M. Nazarychev, Sergey Larin, Alexey Lyulin, Sergey Lyulin, Andrey A. Gurtovenko
Summary: This study explores the potential of chemically modified asphaltene molecules as thermal conductivity enhancers for liquid paraffin, showing promising results for improving the thermal energy storage systems based on paraffin.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
S. V. Larin, V. V. Makarova, S. N. Gorbacheva, M. R. Yakubov, S. V. Antonov, N. I. Borzdun, A. D. Glova, V. M. Nazarychev, A. A. Gurtovenko, S. V. Lyulin
Summary: In this study, polymer additive P3HT was added to paraffin-carbon nanoparticle blends to improve their sedimentation stability, reduce the size of nanoparticle aggregates, and increase the viscosity of the blends. The presence of P3HT had almost no effect on the thermophysical properties of the blends, preserving their critical properties for heat storage applications.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biophysics
Matthew Davies, A. D. Reyes-Figueroa, Andrey A. Gurtovenko, Daniel Frankel, Mikko Karttunen
Summary: A new method combining mixed radial-angular, three-particle correlation function and unsupervised machine learning was used to investigate the emergence of the ripple phase in DPPC lipid bilayers. Data from atomistic molecular dynamics simulations of varying system sizes were analyzed, revealing four distinct conformational populations of lipids. The presence of ordered, disordered, and splayed tail lipids was observed, with spatial clustering of disordered lipids in the groove side of the ripple phase. Principal component analysis confirmed the existence of the four lipid groups.
BIOPHYSICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Victor M. Nazarychev, Artyom D. Glova, Sergey V. Larin, Alexey V. Lyulin, Sergey V. Lyulin, Andrey A. Gurtovenko
Summary: An insight into the impact of cooling rate on phase transformations in molecular systems was gained through computational simulations on organic phase-change materials. It was found that a certain threshold in cooling rates exists, below which the simulations qualitatively reproduced experimental observations, and beyond which the simulations started to deviate considerably from experimental data.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Andrey A. A. Gurtovenko, Victor M. M. Nazarychev, Artem D. D. Glova, Sergey V. V. Larin, Sergey V. V. Lyulin
Summary: In this study, a coarse-grained Martini model was developed to simulate the aggregation behavior of asphaltenes. It was found that native asphaltenes form small clusters that are uniformly distributed in the system, while modified asphaltenes form larger aggregates. Additionally, the mobility of native asphaltenes is slower and the size of aggregates increases with system size.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Artem D. Glova, Victor M. Nazarychev, Sergey V. Larin, Andrey A. Gurtovenko, Sergey V. Lyulin
Summary: Atomistic computer simulations suggest that asphaltenes with enlarged aromatic cores can improve the performance of heat storage devices based on organic phase change materials. Increasing the size of the asphaltene cores promotes the formation of extended structures in paraffin and enhances the thermal conductivity of liquid paraffin.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Andrey A. Gurtovenko, Mikko Karttunen
Summary: This study investigated the interactions between cellulose crystals and model stratum corneum bilayers using molecular dynamics simulations. The findings highlight the critical role of fatty acid protonation in controlling the binding between cellulose and skin.
Correction
Chemistry, Multidisciplinary
Igor V. Volgin, Artyom D. Glova, Victor M. Nazarychev, Sergey V. Larin, Sergey V. Lyulin, Andrey A. Gurtovenko
Article
Chemistry, Multidisciplinary
Artyom D. Glova, Igor V. Volgin, Victor M. Nazarychev, Sergey V. Larin, Sergey V. Lyulin, Andrey A. Gurtovenko
Article
Chemistry, Multidisciplinary
Alexandra Yu. Antipina, Andrey A. Gurtovenko