Article
Chemistry, Physical
Jingyuan Nie, Yibing Deng, Fang Tian, Shengchao Shi, Peng Zheng
Summary: Cation-pi interaction plays a crucial role in biological systems but its experimental verification and quantification at the molecular level are limited. In this study, atomic force microscopy-based single-molecule force spectroscopy was used to measure the stability and kinetics of NGAL protein with cation-pi interactions. The results demonstrated the high-precision detection of weak cation-pi interaction in NGAL.
Review
Chemistry, Multidisciplinary
Alexander F. Pozharskii, Olga Dyablo, Valery A. Ozeryanskii, Olga G. Pogosova
Summary: The review summarizes the progress made in understanding NH center dot center dot center dot pi interactions, which play a significant role in the structuring of proteins, molecular recognition, and drug development. The study of these interactions contributes to a better understanding of complex biochemical processes and the development of targeted drug delivery methods. The review discusses various models and provides examples of reactions and practical applications.
RUSSIAN CHEMICAL REVIEWS
(2022)
Review
Biochemistry & Molecular Biology
Daniel T. Infield, Ali Rasouli, Grace D. Galles, Christophe Chipot, Emad Tajkhorshid, Christopher A. Ahern
Summary: Cation-pi interactions arise from the strong attraction between positively charged entities and the pi-electron cloud of aromatic groups, making them well-suited to the hydrophobic/hydrophilic environment of membrane proteins. As high-resolution structural data of membrane proteins become clearer, cation-pi interactions are increasingly recognized as essential contributors to membrane protein chemistry, function, and pharmacology. Prominent examples demonstrate the significant roles of cation-pi interactions in specialized biological chemistry.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Tariq Sheikh, Shabnum Maqbool, Pankaj Mandal, Angshuman Nag
Summary: The study introduces long-range cation-pi interactions to stabilize hybrid lead halide perovskites in water, achieving complete stability after six months of continuous water treatment without the need for encapsulation. Experimental methods reveal the potential applications of cation-pi interactions in designing more water-stable low-dimensional hybrid perovskite compositions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Huiwen Pang, Chao Ma, Shifeng Zhang
Summary: A novel high temperature defatted soy meal (HSM) adhesive with excellent cold-pressing and hot-pressing adhesion performance, based on mussel-inspired cation-π interactions, is developed as a replacement for aldehyde-based adhesives in wood-based panel production.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Physical
Cesar A. Lopez, Xiaohua Zhang, Fikret Aydin, Rebika Shrestha, Que N. Van, Christopher B. Stanley, Timothy S. Carpenter, Kien Nguyen, Lara A. Patel, De Chen, Violetta Burns, Nicolas W. Hengartner, Tyler J. E. Reddy, Harsh Bhatia, Francesco Di Natale, Timothy H. Tran, Albert H. Chan, Dhirendra K. Simanshu, Dwight V. Nissley, Frederick H. Streitz, Andrew G. Stephen, Thomas J. Turbyville, Felice C. Lightstone, Sandrasegaram Gnanakaran, Helgi I. Ingolfsson, Chris Neale
Summary: The appeal of multiscale modeling approaches lies in the promise of utilizing the synergistic effects between different scales. This paper focuses on multiscale molecular dynamics simulations that combine accuracy and flexibility of fixed-charge all-atom representations with the speed of reductive, coarse-grained representations. The authors introduce an extension to the MuMMI framework and an improved CG-to-AA conversion tool called sinceCG, providing reliable and robust scale conversion.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Materials Science, Multidisciplinary
Huiwen Pang, Rong Yu, Anmin Huang, Xiang Li, Zenghui Xu, Shulin Yin
Summary: A novel short-chain adhesive polymer with excellent underwater adhesion was developed based on topologically enhanced cation-pi interactions. The polymer showed strong cohesion and topologically enhanced cation-pi interactions, leading to excellent underwater adhesion. It also exhibited high-strength hot-melt adhesive properties and maintained its adhesion strength after multiple attachment-detachment cycles.
MACROMOLECULAR MATERIALS AND ENGINEERING
(2022)
Article
Engineering, Environmental
Rui Wang, Ziqi Zhang, Jinquan Suo, Li Liao, Leibo Li, Zhuochen Yu, Heng Zhang, Valentin Valtchev, Shilun Qiu, Qianrong Fang
Summary: Metal-free electrocatalysts based on ionic covalent organic frameworks (COFs) show promising potential for efficient oxygen evolution reaction (OER). A novel COF nanosheet, JUC-627-NS, was introduced as a metal- and pyrolysis-free electrocatalyst by utilizing cationic-pi interactions. The resulting JUC-627-NS@G-2 composite exhibited exceptional OER performance with ultralow overpotential, ranking among the top-performing metal-free electrocatalysts. The imidazolium salt moiety of JUC-627-NS was identified as the active center, while the cation-pi interaction within the complex played a role as a conductive agent.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Polymer Science
Tsukika Momose, Kiho Takeuchi, Haruki Uchida, Shunsuke Saito, Kazuki Nakada, Masato Mutsuga, Aika Yamawaki-Ogata, Yuji Narita, Yohei Kotsuchibashi
Summary: Water-insoluble pH-responsive microfibers were prepared using a specific polymer, which exhibited different charges at different pH values. These microfibers had excellent mechanical properties and stability.
Article
Chemistry, Multidisciplinary
Peiyu Zhang, Huimin Geng, Zhiliang Gao, Jingcheng Hao, Jiwei Cui
Summary: This study reports a one-step assembly method for super-hydrophilic coatings via surface modification with polyphenols and cations based on cation-pi interaction. The coatings exhibit high hydrophilicity, stability, oil resistance, self-cleaning, and anti-fogging properties.
ADVANCED MATERIALS INTERFACES
(2022)
Article
Chemistry, Physical
Hamid Reza Masoodi, Roghayeh Sadat Pourhosseini, Sotoodeh Bagheri
Summary: In this manuscript, the research focuses on investigating the cooperativity between p-p stacking and ion-p interactions in different complexes. The results show that the nature of aromatic ring plays a significant role in the reinforcement or opposite trend of these interactions. It is also found that the presence of both interactions has a stronger effect on p-p stacking compared to ion-p interactions.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Sebastian Spicher, Eike Caldeweyher, Andreas Hansen, Stefan Grimme
Summary: Charged atoms or molecules interacting with pi-systems through ion-pi interactions play a major role in various chemical and biological systems. This study compiled a molecular test set IONPI19 to evaluate different density functional approximations for interaction energies, finding that the double-hybrids PWPB95-D4/QZ and revDSD-PBEP86-D4/QZ are the most reliable methods for describing ion-pi interactions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Lin Zhang, Zongwei Guo, Jiajun Ma, De Sun, Lin Jin, Yuhui Ao, Shicheng Sun
Summary: The challenge of achieving carbon fiber composites with both high strength and toughness can be solved by replicating the nanostructure of nacre into the interface design of carbon fiber. However, constructing a nacre-like interphase on the carbon fiber surface is hindered by the unique nanostructure. To overcome this, a novel self-designed mortar was introduced to trigger the oriented assembly of graphene oxide (GO) on the carbon fiber surface, resulting in a truly bio-inspired interface. The interlaminar shear strength (ILSS) and toughness of the upgraded composites reached 108 MPa and 46.6 MJm(-3), respectively. This work provides new inspiration for designing high-performance carbon-based composites.
APPLIED SURFACE SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Kanagasabai Balamurugan, M. Teresa Pisabarro
Summary: The study reveals the existence of anion-pi interactions between sulfate groups and aromatic amino acids, with protonated histidine showing the strongest interaction. Water molecules play a crucial role in stabilizing the divalent sulfate ions and facilitating these interactions.
Article
Chemistry, Multidisciplinary
Hongbin Huo, Xuedong Xiao, Lu Chang, Xuanchen Xiong, Menghan Shi, Jingxia Wang, Wei Tian
Summary: Constructing two-dimensional supramolecular polymers with complicated hierarchical porosity can control self-assembly architectures and facilitate the fabrication of advanced 2D organic functional materials.
SCIENCE CHINA-CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Mihaly Varadi, Stephen Anyango, David Armstrong, John Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath S. Nair, Lukas Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom Blundell, Kelly P. Brock, Jose Maria Carazo, Jiri Damborsky, Alessia David, Sucharita Dey, Roland Dunbrack, Juan Fernandez Recio, Franca Fraternali, Toby Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivak, Manjeet Kumar, Emmanuel D. Levy, Nir London, Jose Ramon Macias, Madhusudhan M. Srivatsan, Debora S. Marks, Lennart Martens, Stuart A. McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar S. Sorzano, Jan Stourac, Joanna Sulkowska, Radka Svobodova, Natalia Tichshenko, Silvio C. E. Tosatto, Wim Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer Velankar
Summary: PDBe-KB is an open collaboration platform that aims to integrate functional and biophysical annotations from world-leading specialist data resources, serving the Protein Data Bank. By developing standardized data exchange formats and integrating functional annotations from partner resources, PDBe-KB aims to place macromolecular structure data in a biological context and provide valuable biological insights.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Emmanuel Moutoussamy, Qaiser Waheed, Greta Binford, Hanif Khan, Shane Moran, Anna Eitel, Matthew H. J. Cordes, Nathalie Reuter, Nir Ben-Tal, Guanghong Wei
Summary: This study investigates the lipid specificity of SicTox toxins in spider venom. Molecular dynamics simulations reveal that the aromatic cage plays a major role in the binding of toxins to choline headgroups. This is particularly evident in alpha clade PLDs.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Chemistry, Medicinal
Emmanuel E. Moutoussamy, Hanif M. Khan, Mary F. Roberts, Anne Gershenson, Christophe Chipot, Nathalie Reuter
Summary: This study calculated the binding free energy between a peripheral membrane protein and a phospholipid bilayer using a computational method, and compared it with experimental results. The mechanism of the protein's disengagement from the lipid bilayer during interaction separation was also investigated.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Payal Chatterjee, Mert Y. Sengul, Anmol Kumar, Alexander D. MacKerell
Summary: The outcomes of computational chemistry and biology research are greatly influenced by the choice of forcefield used in molecular simulations. This study develops a deep learning-based framework for optimizing van der Waals interactions in molecular simulations. The resulting LJ parameters (interactions between atoms) are validated for their performance in reproducing condensed phase thermodynamic properties and demonstrate improved accuracy in reproducing solvent and crystal properties.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Medicinal
Asuka A. Orr, Suliman Sharif, Junmei Wang, Alexander D. MacKerell
Summary: Generalized force fields (FFs) are extensions of biomolecular FFs used for organic molecules. However, their application to arbitrary molecules requires caution to ensure their integrity.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Abhishek A. Kognole, Anthony Hazel, Alexander D. MacKerell
Summary: RNA molecules can be potential drug targets in various diseases due to their dysregulated expression or misfolding. Noncoding RNAs, which account for a large part of the human genome, have complex structures and can be targeted by small molecules. The SILCS computational approach, termed SILCS-RNA, was extended to target RNA in this study and evaluated against seven RNA targets. The method provides detailed functional group affinity patterns and facilitates the identification of new potential binding sites and ligand design.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biophysics
Meruyert Kudaibergenova, Jiqing Guo, Hanif M. Khan, James Lees-Miller, Mahdi Mousaei, Williams Miranda, Van A. Ngo, Sergei Yu Noskov, Henry J. Duff
Summary: This study discovered a cationic leak current known as omega current, which arises from mutations of the first charged residue in the S4 of the voltage sensor domains of sodium and potassium voltage-gated channels. By mutating the first charged residue of hERG1, researchers discovered a novel omega current. Molecular dynamics simulations and replica-exchange umbrella sampling simulations revealed the atomistic underpinnings of this mechanism.
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Physical
Wenbo Yu, David J. Weber, Alexander D. MacKerell
Summary: Covalent drug design plays a significant role in drug discovery by forming a covalent bond with targeted residues, leading to a more effective therapeutic approach. Computational methods can identify reactive residues, test potential reactivities, and predict noncovalent contributions to binding. SILCS, a functional group mapping approach, considers protein flexibility, functional group, and protein desolvation along with functional group-protein interactions. SILCS-Covalent, an integrated workflow, can qualitatively and quantitatively inform covalent drug discovery.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor, Benoit Roux, Alexander D. MacKerell Jr, Jeffery B. Klauda
Summary: Accurate empirical force fields of lipid molecules are crucial for molecular dynamics simulations of various lipid systems and heterogeneous systems. The polarizable Drude force field has been optimized in this study to improve its accuracy in simulating pure bilayers and membranes. By using both experimental and quantum mechanical data, the optimized force field shows good agreement with a range of experimental observables. The polarizable Drude2023 force field is anticipated to advance our understanding of electronic polarization in lipid systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Mingtian Zhao, Abhishek A. Kognole, Sunhwan Jo, Aoxiang Tao, Anthony Hazel, Alexander D. MacKerell Jr
Summary: In this study, the sampling efficiency of the GCMC method was improved by applying known cavity-bias and configurational-bias algorithms on GPU architecture. The method was parallelized using CUDA and OpenCL, resulting in simultaneous sampling of a large number of configurations during insertion attempts. The partitioning scheme allowed for simultaneous insertion attempts for large systems, significantly improving efficiency. The algorithm was shown to be useful in the application of the site-identification by ligand competitive saturation (SILCS) co-solvent sampling approach for the protein CDK2.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Medicine, Research & Experimental
Asuka A. Orr, Aoxiang Tao, Olgun Guvench, Alexander D. MacKerell
Summary: Protein-based therapeutics often face challenges of protein aggregation and high solution viscosity due to high concentrations of active protein. The charge of a protein, affected by its environment, plays a significant role in these solution behaviors. This study presents a structure-based approach called SILCS-Biologics, which predicts the effective charge of proteins by considering the competition between ions and the presence of buffers.
MOLECULAR PHARMACEUTICS
(2023)
Article
Chemistry, Multidisciplinary
Mert Y. Sengul, Alexander D. MacKerell
Summary: Metal ions, particularly Mg2+, play a role in stabilizing RNA's tertiary structures. However, the atomic-level mechanisms underlying this process are not fully understood. In this study, computational techniques were combined to investigate the specific interactions between Mg2+ ions and RNA, particularly in the pseudoknot structure of the Twister ribozyme.
Article
Chemistry, Multidisciplinary
Himanshu Goel, Wenbo Yu, Alexander D. MacKerell
Summary: This article presents the application of structure- and ligand-based approaches in simulating and predicting hERG drug liability. By combining the SILCS method with physicochemical properties, predictive models for hERG blockade were developed, resulting in improved predictability and aiding in rational drug design to minimize hERG risk.
CHEMISTRY-SWITZERLAND
(2022)
Article
Chemistry, Multidisciplinary
Mert Y. Sengul, Alexander D. MacKerell
Summary: The presence of polarizability in the force field improves the stability of RNA hairpin structures and leads to variations in dipole moments and ion distribution. Molecular dynamics simulations play a crucial role in modeling biomolecular systems, and the treatment of electrostatic interactions in the force field strongly affects simulation accuracy. In this study, the impact of polarization on structural properties, dipole moment distributions, and cation interactions in RNA hairpin systems is investigated using polarizable and non-polarizable nucleic acid force fields.
JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY
(2022)
