Article
Biochemistry & Molecular Biology
Abhishek Kumar Singh, Boris Schade, Marta Rosati, Rashmi Rashmi, Valentina Dichiarante, Gabriella Cavallo, Pierangelo Metrangolo, Rainer Haag
Summary: Amphiphiles containing fluorinated segments form structures of lower curvature in aqueous solution, which allows for better visualization of their high electron density in cryo-TEM. A modular approach has been developed for the synthesis of nonionic branched amphiphiles, and the aggregation behavior of these structures has been investigated using DLS and cryo-TEM. The results show the formation of multivesicular and multilamellar vesicles, as well as smaller unilamellar vesicles. Furthermore, cell viability tests demonstrate the low toxicity of these nanoarchitectures for potential biomedical applications.
MACROMOLECULAR BIOSCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Bailey J. Richardson, Chao Zhang, Pascal Rauthe, Andreas-Neil Unterreiner, Dmitri V. Golberg, Berwyck L. J. Poad, Hendrik Frisch
Summary: By exploiting self-assembled environments, inefficient reactions can be transformed into highly efficient reactions, leading to an expansion of the toolbox for bioorthogonal chemistry. Through the incorporation of peptide sequences, the assembly of structures with both hydrophilic and hydrophobic regions enables a highly efficient photoligation reaction within a defined local environment. The reversible morphology change allows for the control of the photoligation reaction, by switching it on or off simply by adjusting the pH.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Polymer Science
Thomas Babut, Mona Semsarilar, Marc Rolland, Damien Quemener
Summary: In this study, a waterborne approach was proposed to co-assemble peptide amphiphiles (PA) and polyelectrolytes into porous membranes with nanostructured networks. Various production methods were explored to shape the material and optimize the structure, leading to a membrane material in the ultrafiltration range with a pore radius of about 7.6 nm.
Article
Chemistry, Multidisciplinary
Nils Baeumer, Soichiro Ogi, Lorenz Borsdorf, Shigehiro Yamaguchi, Gustavo Fernandez
Summary: We demonstrate that desymmetrization of a hydrophobic chromophore can effectively modulate aromatic interactions and exciton coupling during self-assembly. Consequently, multiple assembled states are accessible, providing a straightforward method to introduce pathway complexity in aqueous environments.
CHEMICAL COMMUNICATIONS
(2023)
Review
Chemistry, Multidisciplinary
Shuichi Hiraoka, Satoshi Takahashi, Hirofumi Sato
Summary: The collaboration of experiment and theory is crucial in science and technology, as shown in the investigation of molecular self-assembly process. The development of QASAP experimental method and NASAP numerical approach allows for detailed analysis and prediction of molecular self-assembly pathways and outcomes based on varying reaction conditions. The future direction in artificial molecular self-assembly focuses on pathway-dependent self-assembly and kinetic control.
Article
Biochemistry & Molecular Biology
Fang-Yi Wu, Hsin-Chieh Lin
Summary: Synthetic bioactive aromatic peptide amphiphiles are recognized as key elements of emerging biomedical strategies due to their biocompatibility, design flexibility, and functionality. We investigated the self-assembly driving force of two supramolecular materials and found ordered π-π interactions and secondary structures in both compounds. In cell experiments, PFB-IKVAV showed promise as a potential supramolecular biomaterial for biomedical applications.
Article
Chemistry, Multidisciplinary
Jing Sun, Julian Vogel, Lisa Chen, A. Lennart Schleper, Tim Bergner, Alexander J. C. Kuehne, Max von Delius
Summary: In this study, we synthesized ribose- and ribonucleotide-based amphiphiles and investigated their self-assembly and reactivity. We found that these amphiphiles can form various types of aggregates with aggregation-induced emission properties in both solution and solid state. Additionally, we discovered that the addition of a specific reagent can promote rapid dimerization of the amphiphiles, reducing their critical aggregation concentration. These findings may have implications for simulating the formation of primitive compartments under prebiotic conditions.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Applied
Anson Kwok-Hei Chau, Leong-Hung Cheung, Franco King-Chi Leung
Summary: The red-light sensitivity of amphiphiles in aqueous media can be restored by co-assembling with stiff stilbene amphiphiles, and the morphological changes of these supramolecular structures can be fine-tuned by red-light irradiation.
Article
Chemistry, Multidisciplinary
Zhenfei Gao, Tiannan Wang, Zikun Rao, Hui Yan, Ran Zhang, Guosong Chen
Summary: Supra-amphiphilic compounds containing disaccharides and azobenzene ends were constructed via dynamic covalent bond. The slight structural difference of the disaccharides was found to significantly affect the self-assembled morphologies. Three kinds of azo-disaccharide supra-amphiphiles were found to assemble into different morphologies with only a difference in chemical structure. Molecular simulation revealed that the packing of molecules was influenced by the contribution from hydrogen bonds. This study highlights the importance of saccharide packing, particularly related hydrogen bonding, in determining the final morphology of assembled structures.
CHINESE CHEMICAL LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Yawei Sun, Jiaqi Zhang, Feng Liu, Qilu Zhang
Summary: Rapid and scalable self-assembly of an amphiphilic 21-arm star copolymer, (polystyrene-block-polyethylene glycol)(21), in aqueous solution has been achieved using reverse solvent exchange procedure. The resulting nanoparticles show narrow size distribution, which is confirmed by transmission electron microscope (TEM) and nanoparticle tracking analysis (NTA). The kinetic-controlled self-assembly mechanism of the copolymers involves the star topology of the amphiphilic copolymer and deep quenching condition during phase separation.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Applied
Sagnik De, Gopal Das
Summary: The water-soluble substituted thiourea amphiphile can detect mercury with high selectivity and sensitivity among other metal ions in water. Its structure allows for self-assembly into specific morphology which can be observed through microscopic analysis. Real sample testing has shown its selective recognition capability towards sulphide ion.
Article
Chemistry, Multidisciplinary
Guoxin Lu, Guiqiang Zhu, Qian Zhang, Pan Tian, Mengjiao Cheng, Feng Shi
Summary: In this study, a supra-amphiphile Marangoni fuel-sodium-4-(benzylideneamino) benzenesulfonate (SBBS) was synthesized, which can be hydrolyzed in a timely manner to a species without surface activity, thus extending the motion time by 10-fold and achieving self-assembly of millimeter-scaled components. The underlying mechanism was explained through motion analyses and simulation. This strategy provides an active solution for self-assembly at the mu m-to-mm scale and promotes interactive ideas between miniaturized chemical robots.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Rie Wakabayashi, Ayato Higuchi, Hiroki Obayashi, Masahiro Goto, Noriho Kamiya
Summary: This study investigated the self-assembly and enzymatic post-modification of short aromatic peptide amphiphiles, showing that these molecules can form fibrous structures and their assembly is influenced by solution pH. Moreover, enzymatic reactions showed different rates at varying pH, indicating pH dependency in the enzyme-catalyzed post-modification process.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Inorganic & Nuclear
Jia-Jun Jiang, Anson Kwok-Hei Chau, Man-Kin Wong, Franco King-Chi Leung
Summary: Supramolecular assemblies of gold complex-based amphiphiles in aqueous media are sensitive to external environments, making them attractive for applications in soft functional materials. This study demonstrates a reversible supramolecular assembly of gold (III) amphiphiles controlled by counterions, and their co-assembly with gold nanoparticles.
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY
(2022)
Review
Chemistry, Multidisciplinary
Qinglin Yang, Weiwei Xu, Ming Cheng, Siyun Zhang, Elena G. Kovaleva, Feng Liang, Demei Tian, Jun-an Liu, Reda M. Abdelhameed, Jing Cheng, Haibing Li
Summary: This feature article summarizes the advances in stimuli-responsive pillararene modified nanosystems for controlled drug release, including decomposition release and gated release. The control principles of these nanosystems are discussed in detail.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Hanlin Gu, Wei Wang, Siqin Cao, Ilona Christy Unarta, Yuan Yao, Fu Kit Sheong, Xuhui Huang
Summary: The paper presents a new method based on RPnet to cluster microstates into macrostates for analyzing the conformational dynamics of biological macromolecules. Through the reverse-projection scheme and neural network, successful analysis of dynamics of 2D potential, alanine dipeptide, and RNA polymerase was achieved.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Review
Biochemistry & Molecular Biology
Ilona Christy Unarta, Eshani C. Goonetilleke, Dong Wang, Xuhui Huang
Summary: RNA polymerase II (Pol II) incorporates complementary ribonucleotides into the growing RNA chain one at a time and ensures transcriptional fidelity by backtracking and cleaving misincorporated nucleotides. Recent studies have made progress in understanding the catalytic mechanisms of Pol II, including the two-metal-ion mechanism for nucleotide addition and the role of Pol II residues in facilitating the catalysis. Interestingly, Pol II relies on its residues to recognize misincorporated nucleotides during backtracking before cleavage, effectively compartmentalizing its dual catalytic functions using the same active site.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Yifan Dai, Mina Farag, Dongheon Lee, Xiangze Zeng, Kyeri Kim, Hye-in Son, Xiao Guo, Jonathan Su, Nikhil Peterson, Javid Mohammed, Max Ney, Daniel Mark Shapiro, Rohit V. Pappu, Ashutosh Chilkoti, Lingchong You
Summary: The formation of biomolecular condensates through associative and segregative phase transitions is crucial for controlling cellular functions. This inspired the design of synthetic systems, but most research has focused on phase behaviors in a test tube. In this study, a rational engineering approach was used to program the formation and physical properties of synthetic condensates, achieving specific cellular functions such as plasmid sequestration and transcription regulation in bacteria, and protein circuit modulation in mammalian cells. This approach lays the foundation for engineering designer condensates for synthetic biology applications.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biophysics
Mina Farag, Alex S. Holehouse, Xiangze Zeng, Rohit V. Pappu
Summary: Biomolecular condensates form through phase transitions of biomacromolecules specific to the condensates. Intrinsically disordered regions with appropriate sequence grammars can contribute to the driving forces for phase separation of multivalent proteins through homotypic and heterotypic interactions. Experiments and computations have advanced to the point where the concentrations of coexisting dense and dilute phases can be measured or computed for individual intrinsically disordered regions. The development of computational tools like FIREBALL enables efficient analysis and fitting of experimental or computed data of binodals, providing insight into the coil-to-globule transitions of macromolecules.
BIOPHYSICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Xiangze Zeng, Rohit V. Pappu
Summary: Biomolecular condensates are specific cellular structures that can organize cellular matter and biochemical reactions in space and time. They are formed and dissolved through spontaneous and driven phase transitions of multivalent associative macromolecules. Current progress has focused on modeling sequence-specific phase transitions, especially for intrinsically disordered proteins. In this review, we summarize the state-of-the-art theories and computations aimed at understanding and modeling sequence-specific, thermodynamically controlled, coupled associative and segregative phase transitions of archetypal multivalent macromolecules.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Chemistry, Physical
Kirill A. Konovalov, Cheng-Guo Wu, Yunrui Qiu, Vijaya Kumar Balakrishnan, Pankaj Singh Parihar, Michael S. O'Connor, Yongna Xing, Xuhui Huang
Summary: Mutations in protein phosphatase 2A (PP2A) disrupt its autoinhibition and phosphorylation-induced activation, leading to intellectual disability and cancer. Allosteric pathway analysis and biochemical experiments reveal that the disease mutant E198K weakens the stabilizing pathways of the regulatory subunit B56d, while the mutant E200K induces exposure of the active site. Remarkably, the allosteric pathways of E198K resemble those in phosphorylation-activated WT, suggesting a conserved mechanism for alleviating autoinhibition.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Siqin Cao, Michael L. L. Kalin, Xuhui Huang
Summary: Integral equation theory (IET) is an effective solvation model that provides computational efficiency and accuracy. We have developed a new software package called EPISOL, which utilizes 3D-RISM calculations to obtain solvation structure and free energies of solute molecules in different solvents. EPISOL features various closures, free energy functionals, and numerical schemes to enhance stability and convergence. It is compatible with AMBER and GROMACS simulation packages and can efficiently handle large biomolecules. EPISOL is a valuable tool for calculating solvation density distributions and solvent free energy in chemical and biological systems.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Anthony J. Dominic III, Siqin Cao, Andres Montoya-Castillo, Xuhui Huang
Summary: Conformational changes in biomolecular systems are essential for their function and understanding these changes can have significant implications for drug discovery and bioengineering applications. While Markov state models have provided insights into slow conformational dynamics, this Perspective highlights the importance of incorporating memory effects to improve computational efficiency and accuracy. Various techniques such as Fokker-Planck equations, recurrent neural networks, and generalized master equations, which consider memory effects, are discussed in this article.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Eric M. M. Kohn, Kirill Konovalov, Christian A. A. Gomez, Gillian N. N. Hoover, Andrew Kai-hei Yik, Xuhui Huang, Jeffrey D. D. Martell
Summary: This study demonstrates the utility of terminal alkynes in improving the binding properties of DNA aptamers to proteins. The terminal alkyne enhances the binding affinity by stabilizing the aptamer-protein interface through noncovalent interactions. This is the first case of terminal alkynes enhancing the binding properties of an aptamer.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Physical
Siqin Cao, Yunrui Qiu, Michael L. Kalin, Xuhui Huang
Summary: The generalized master equation (GME) is a powerful method for studying biomolecular dynamics. We present a new method, the Integrative GME (IGME), which analytically solves the GME when the memory kernels have decayed to zero, overcoming the challenges of the quasi Markov State Model (qMSM).
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Bojun Liu, Mingyi Xue, Yunrui Qiu, Kirill A. Konovalov, Michael S. O'Connor, Xuhui Huang
Summary: Identifying slow collective variables (CVs) in self-assembly dynamics is challenging due to permutation and rotational symmetries as well as the out-of-equilibrium nature. In this study, GraphVAMPnets, a combination of graph neural networks and variational Markovian process theory, is utilized to overcome these challenges and identify the slow CVs in self-assembly processes of two systems. The method proves effective in capturing the essential dynamics of self-assembly.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Yunrui Qiu, Michael S. O'Connor, Mingyi Xue, Bojun Liu, Xuhui Huang
Summary: Conformational changes are crucial in chemical and biological processes, but analyzing complex conformational changes can be challenging due to the vast number of kinetic pathways involved. To address this issue, researchers have developed a path classification algorithm (LPC) that efficiently groups parallel kinetic pathways into distinct metastable path channels, making them easier to comprehend.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Xiaowei Wang, Tiantian Xu, Yuan Yao, Peter Pak-Hang Cheung, Xin Gao, Lu Zhang
Summary: This study utilizes molecular dynamics simulations to construct a Markov state model and investigate the translocation dynamics of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). The research reveals the key steps of translocation and the asynchronous movement of the template-primer duplex, providing new insights into viral replication and transcription.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Gable M. Wadsworth, Walter J. Zahurancik, Xiangze Zeng, Paul Pullara, Lien B. Lai, Vaishnavi Sidharthan, Rohit V. Pappu, Venkat Gopalan, Priya R. Banerjee
Summary: Co-phase separation of RNAs and RNA-binding proteins is an important driving force for the biogenesis of ribonucleoprotein granules. It has been discovered that RNA can also undergo phase transitions in the absence of proteins, driven by entropy and modulated by RNA bases. The presence of magnesium ions enables RNA-only condensates to also undergo percolation transitions, leading to arrested condensates.
Article
Chemistry, Inorganic & Nuclear
Xujie Qin, Quan Zhou, Zhe-Ning Chen, Lu Zhang
Summary: Heterocyclic aromatic compounds, as important members of benzene-like aromatic compounds, have wide applications in catalysis, functional materials, and biopharmaceuticals. Introducing a heteroatom in metalla-aromatic compounds provides an opportunity to create new aromatic functional materials. Our study reveals that the unexpected geometric bending in heterometallabenzenes can be well explained by our previously proposed σ-dominated scheme, and introducing an isolobal heteroatom in the C-5 ring leads to a more significant bending and enhanced aromaticity. Overall, our investigation extends the validity of the σ-dominated scheme and provides an approach for the rational designing of organometallic-based functional materials with fascinating aromaticity.