Editorial Material
Multidisciplinary Sciences
Jyoti Madhusoodanan
Summary: Automated microscopes that adjust to the unique characteristics of each sample can accurately capture elusive biological phenomena with high level of detail.
Article
Chemistry, Analytical
Deseree J. Reid, Tapasyatanu Dash, Zhihan Wang, Craig A. Aspinwall, Michael T. Marty
Summary: Daptomycin is a cyclic lipopeptide antibiotic that interacts with lipid membranes in a non-specific manner. The interaction strength depends on membrane rigidity, with more rigid membranes showing stronger interactions. More fluid membranes may undergo pore formation to expose daptomycin to oxidation. These findings highlight the complementary use of native mass spectrometry, fast photochemical oxidation of peptides, and membrane conductance experiments in studying antibiotic-membrane interactions.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Vyshnavi Vennelakanti, Helena W. Qi, Rimsha Mehmood, Heather J. Kulik
Summary: Hydrogen bonds play a crucial role in the structure and catalytic action of enzymes, with amino acid sidechains containing functional groups that can act as both hydrogen bond acceptors and donors. Through calculations and analysis of model systems, it has been shown that structures with ambifunctional hydrogen bonds in proteins provide energetic benefits, despite geometric constraints and many-body electronic effects.
Article
Biophysics
Yutaka Murata, Toru Niina, Shoji Takada
Summary: Liquid-liquid phase separation (LLPS) has been widely studied in recent years for explaining the formation of cellular biomolecular condensates. Molecular simulation methods, such as the stoichiometric interaction (SI) potential, have been used to gain insights into the structures of these complex components. However, the SI potential alone cannot quantitatively reproduce the phase diagram of LLPS, and the combination of SI and pairwise interactions is necessary. Biomolecular condensates with mixed SI and pairwise interactions exhibit fluidity, while those with pairwise interactions alone do not show detectable diffusion. The phase diagrams obtained from simulations using different numbers of tandem domains agree quantitatively with experimental results.
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Analytical
Deseree J. Reid, Tapasyatanu Dash, Zhihan Wang, Craig A. Aspinwall, Michael T. Marty
Summary: In this study, native mass spectrometry (MS) and fast photochemical oxidation of peptides (FPOP) were used to investigate the interactions between the antibiotic daptomycin and different lipid bilayer nanodiscs. The results showed that daptomycin incorporates randomly into bilayers and has stronger interactions with rigid membranes. Pore formation may occur in fluid membranes, exposing daptomycin to oxidation. These findings demonstrate the complementarity of native MS, FPOP, and membrane conductance experiments in understanding antibiotic peptide-membrane interactions.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Man Wu, Guang Xu, Chong Han, Peng-Fei Luan, Yu-Hang Xing, Fang Nan, Liang-Zhong Yang, Youkui Huang, Zheng-Hu Yang, Lin Shan, Li Yang, Jiaquan Liu, Ling-Ling Chen
Summary: In this study, it was found that individual spherical FC/DFC units in human cells are coated by DDX21, and the long noncoding RNA SLERT promotes DDX21 to adopt a closed conformation and form loose clusters, impacting ribosomal RNA production.
Article
Biochemical Research Methods
Benjamin G. Weiner, Andrew G. T. Pyo, Yigal Meir, Ned S. Wingreen
Summary: This research shows that the sequence of binding motifs strongly influences the ability of biomolecular condensates to phase separate, with sequences containing large blocks of identical motifs promoting phase separation. Specific interacting motifs affect the formation of self-bonds, rather than bonds between polymers, controlling the phase separation process. This provides a new entropy-based mechanism for the biological control of phase separation.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Chemistry, Physical
Amnon Horovitz, Tridib Mondal
Summary: Hill coefficients can be determined for equilibrium and transient kinetic data to provide insights into allosteric mechanisms. The ratio of equilibrium and kinetic Hill coefficients can indicate concerted or sequential transitions, with implications for symmetric dimers and homooligomers in ligand binding.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Multidisciplinary Sciences
Andrew Z. Lin, Kiersten M. Ruff, Furqan Dar, Ameya Jalihal, Matthew R. King, Jared M. Lalmansingh, Ammon E. Posey, Nadia A. Erkamp, Ian Seim, Amy S. Gladfelter, Rohit V. Pappu
Summary: The authors report that protein-RNA condensates with shared proteins and distinct RNAs can form and persist in vitro and in cells as distinct entities if the nonshared RNA molecules are dynamically arrested, but the shared protein components are dynamically exchangeable.
NATURE COMMUNICATIONS
(2023)
Article
Geology
Ari H. D. Koeppel, Christopher S. Edwards, Andrew M. Annex, Kevin W. Lewis, Gabriel J. Carrillo
Summary: The light-toned sedimentary layers in Mars' Southern Highlands have long been a mystery in uncovering the planet's climatic history. The role of water in their formation is debated and their elevated thermal inertia raises questions about the strength of the materials. By studying the relationships between thermal inertia, mineralogy, erosion susceptibility, and cohesion, researchers find that variations in dust cover and eolian abrasion can affect apparent thermal inertia. The results suggest that water-rich surface conditions in the region may have been intermittent and fleeting.
Article
Gerontology
Emily Brooks, Somayyeh Mohammadi, W. Ben Mortenson, Catherine L. Backman, Chihori Tsukura, Isabelle Rash, Janice Chan, William C. Miller
Summary: The COVID-19 pandemic has resulted in increased social isolation and reduced participation in older adults. This longitudinal qualitative study examined the experiences of adults aged 65+ through a series of four semi-structured interviews. The findings revealed that older adults went through a process of struggling, adapting, and appreciating during the pandemic. Engagement in meaningful activities and high-quality social interactions were crucial for promoting well-being in older adults, emphasizing the need for policies and services to support engagement during global crises.
JOURNAL OF APPLIED GERONTOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Zahoor Ahmed, Hasan Zulfiqar, Lixia Tang, Hao Lin
Summary: The study found that polar amino acids, short bond length, wide DHA angle, and aromatic amino acids play important roles in the thermostability of proteins through statistical analysis on pairs of thermophilic proteins and their non-thermophilic orthologous.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Ayushi Awasthi, Isaac F. Leach, Silene Engbers, Rakesh Kumar, Raju Eerlapally, Sikha Gupta, Johannes E. M. N. Klein, Apparao Draksharapu
Summary: Cytochrome P450s and Galactose Oxidases utilize redox active ligands to generate reactive high-valent intermediates for oxidation reactions. In this study, Ni-II(salen) was oxidized with mCPBA to produce a transient Ni-III bisphenoxyl diradical species. Spectroscopic analyses revealed oxidation events on both the ligand and the metal center, supporting the formation of the Ni-III bisphenoxyl diradical species. DFT calculations confirmed the electronic structure and d-configuration of the metal center consistent with this species. The resulting three-electron oxidized species is capable of hydrogen atom abstraction and oxygen atom transfer reactions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Biochemistry & Molecular Biology
Jeremy D. Schmit, Marina Feric, Miroslav Dundr
Summary: Biomolecular condensates are present throughout the cell and serve various biochemical functions. The optimization of condensate functionality relies on a wide range of interactions driving condensation, involving both strong and weak affinities. This is illustrated by examples such as the nucleolus, SPOP/DAXX condensates, and chromatin, where a hierarchical assembly motif of weak, transient interactions condense structurally defined functional units.
TRENDS IN BIOCHEMICAL SCIENCES
(2021)
Article
Chemistry, Physical
Paul Stritt, Michael Jawurek, Karin Hauser
Summary: Membranes are crucial for the functionality of membrane proteins, and time-resolved infrared spectroscopy enables the investigation of interaction-induced dynamics of the protein and the lipid membrane. By utilizing deuterated lipid alkyl chains, we can monitor lipid dynamics during the photoreaction of bacteriorhodopsin. Our home-built quantum cascade laser-based IR spectrometer covers all relevant spectral regions and allows for better signal-to-noise ratio and nanosecond time resolution. QCL spectroscopy extends the study of the protein's photocycle toward dynamics of the interacting membrane.
JOURNAL OF CHEMICAL PHYSICS
(2023)
