Review
Biochemistry & Molecular Biology
Samantha A. Miles, Joshua Andrew Nillama, Luke Hunter
Summary: This review summarizes the applications of side chain-fluorinated amino acids in medicinal chemistry and protein science. The paper outlines strategies for incorporating fluorine atoms into amino acid side chains and elaborating these building blocks into more complex fluorinated peptides and proteins. It then describes the diverse benefits of fluorine in amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.
Article
Biochemistry & Molecular Biology
Denis V. Petrovskiy, Kirill S. Nikolsky, Vladimir R. Rudnev, Liudmila I. Kulikova, Tatiana V. Butkova, Kristina A. Malsagova, Arthur T. Kopylov, Anna L. Kaysheva
Summary: This paper discusses the impact of post-translational modifications and amino acid substitutions on the 3D structure of proteins and focuses on predicting accurate PTMs in proteins. The study also compares algorithmic solutions with existing structure modeling packages and explores their potential for further development and optimization.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Nanoscience & Nanotechnology
Mikayla E. Barry, Pinar Aydogan Gokturk, Audra J. DeStefano, Amanda K. Leonardi, Christopher K. Ober, Ethan J. Crumlin, Rachel A. Segalman
Summary: Polymers are widely used in various applications that involve water exposure, and understanding the surface chemistry of polymers in these conditions is crucial. This study investigates the effects of surface-active side chains on polymer surface chemistry and water sorption using synchrotron ambient pressure X-ray photoelectron spectroscopy. The results show that different types of side chains, as well as the polymer backbone and environmental conditions, influence the water sorption behavior of the polymers.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Physical
Taegun Park, Taehyeon Kim, Jongwon Han, Sangwoo Lim
Summary: The improvement of Si3N4 etching kinetics and suppression of oxide regrowth are crucial in the selective Si3N4 etching process for the fabrication of 3D NAND devices on multi-layered Si3N4/SiO2 structures. By reducing the concentration of H3PO4, oxide regrowth was suppressed and 30 wt% H3PO4 showed the highest Si3N4/SiO2 etching selectivity. Additionally, introducing amino acids with hydrophilic side chains into 30 wt% H3PO4 increased the Si3N4 etching rate and suppressed oxide regrowth.
APPLIED SURFACE SCIENCE
(2023)
Article
Chemistry, Organic
Joomyung Jun, Ronald T. Raines
Summary: The synthesis of alpha-aryl-alpha-diazoamides was achieved through a two-step process involving Pd-catalyzed C-H arylation and aminolysis, enabling the esterification of carboxyl groups in aqueous solution to become substrates for an esterase. This broad synthetic route paves the way for further development of diazo compounds in chemical biology.
Article
Chemistry, Multidisciplinary
Hung V. -T. Nguyen, Yivan Jiang, Somesh Mohapatra, Wencong Wang, Jonathan C. Barnes, Nathan J. Oldenhuis, Kathleen K. Chen, Simon Axelrod, Zhihao Huang, Qixian Chen, Matthew R. Golder, Katherine Young, Dylan Suvlu, Yizhi Shen, Adam P. Willard, Michael J. A. Hore, Rafael Gomez-Bombarelli, Jeremiah A. Johnson
Summary: This study synthesized water-soluble chiral bottlebrush polymers using macromonomers of different rigidity, and discovered that polymers with conformationally flexible mirror image side chains exhibited significant differences in properties compared to those with comparably rigid mirror image side chains. The observations were rationalized by correlating greater conformational freedom with enhanced chiral recognition, providing insights for the design of future biomaterials.
Article
Chemistry, Physical
Giuseppe Graziano
Summary: Experimental measurements show that the Gibbs energy change is negative when amino acid side chains are transferred from water to liquid N-methylacetamide. However, the rationalization of these data is currently lacking. Classic scaled particle theory calculations suggest that the reversible work to create molecular-sized cavities is greater in water than in N-methylacetamide, offering a physically reliable rationale for this phenomenon.
CHEMICAL PHYSICS LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Ashita Ohri, Preethi P. Seelam, Purshotam Sharma
Summary: This study utilizes density functional theory calculations to analyze the features and strength of hydrogen-bonded complexes between RNA nucleobase edges and polar amino acid side chains, uncovering various types of complexes and their strength in both gas and solvent phases. The ability of these complexes to provide stability to RNA-protein complexes is highlighted, along with the significance of complexes involving protonated nucleobases and weakly polar cysteine side chains in biological processes involving RNA-protein interactions. The study also reveals the greater strength of interactions between amino acid side chains and base pairs compared to base-amino acid interactions, providing a basis for understanding nucleic acid-protein interactions and potential applications in algorithm design for automated search at the RNA-protein interface.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Chemistry, Physical
Ce Wang, Pingping Zhang, Zhenghong Chen, Yang Liu, Li Zhao, Nan Wang, Baocai Xu
Summary: Amino acid surfactants derived from vegetable oils have diverse properties due to various fatty acyl groups, with structural characteristics such as fatty acyl chain length, number of C=C bonds, and hydroxyl substituent affecting interfacial properties. Longer fatty acyl chains enhance intermolecular interactions, while C=C bonds in oleoyl and inoleoyl chains and hydroxyl groups on ricinoleoyl influence the compactness and viscoelasticity of interfacial films. The findings provide insights into the design and application of N-acyl amino acid surfactants.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Physical
Akihisa Miyagawa, Gaku Fukuhara, Tetsuo Okada
Summary: This study evaluated the pressure dependencies of the acid dissociation constants (pK(a)) of pH indicator dyes and amino acids, confirming a positive correlation between the molar volume difference (ΔV°) and the molar compressibility difference (Δκ) data. The relationship is discussed based on structural changes in molecules upon deprotonation and associated hydration changes, suggesting a contraction of the hydration sphere by deprotonation leads to negative ΔV° and Δκ.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Multidisciplinary Sciences
Matea Hajnic, Santiago Alonso Gil, Anton A. Polyansky, Anita de Ruiter, Bojan Zagrovic
Summary: Covalent modifications of standard DNA/RNA nucleobases affect epigenetic regulation of gene expression by modulating interactions between nucleic acids and protein readers. This study derives the absolute binding free energies and analyzes the binding modalities between key modified nucleobases (5mC, 5hmC, m(6)A) and non-prolyl/non-glycyl protein side chains. The results provide insights into understanding and modulating the interactions between modified nucleic acids and proteins.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Valentin Nelea, Jeanne Paquette, Marc D. McKee
Summary: Phosphorylation of amino acids in proteins plays a crucial role in mineralization of tissues and structures; phosphorylation of phosphoproteins like osteopontin regulates mineralization in calcium phosphate and calcium carbonate tissues; small phospho-molecules interact with calcite during dissolution, leading to nanotopographic surface alterations.
CRYSTAL GROWTH & DESIGN
(2021)
Article
Chemistry, Multidisciplinary
Russell G. Wells, Katriel D. Sahlstrom, Kraig A. Wheeler
Summary: A new method of cocrystallizing hydrogen oxalate with pairs of amino acid quasienantiomers containing a sulfur atom has been developed, resulting in new quasiracemic materials with unique crystal packing arrangements. Despite variations in components, these structures exhibit a high degree of isostructurality and form charge-assisted hydrogen-bonded networks that thermodynamically favor crystal packing.
Article
Chemistry, Physical
Santanu Santra, Shakuntala Dhurua, Madhurima Jana
Summary: Amino acids with basic side chains are known to increase the stability of proteins in their native-folded state, however, the efficiency and molecular mechanism behind this process are still controversial. A study using molecular dynamics simulations found that arginine, histidine, and lysine solutions have varying effects on the hydration and conformational stability of the insulin monomer. Arginine was observed to influence insulin stability by enhancing the exclusion of water molecules from the protein surface, leading to more rigid conformations compared to histidine and lysine.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Charles A. Lewis, Richard Wolfenden
Summary: SAM is a powerful methylating agent that evolved to modify specific lysine residues in proteins and transcription factors. The methyl transfer reactions are insensitive to pH changes and each step in the process has a similar change in free energy value.
Article
Biochemistry & Molecular Biology
Hsiao-Chieh Tsai, Ching-Hong Huang, Ling-Hsien Tu
Summary: Islet amyloid polypeptide (IAPP) is a polypeptide hormone co-secreted with insulin by pancreatic beta-cells. It tends to aggregate into soluble oligomers, which are considered one of the hallmarks of type II diabetes. This study successfully grafted the aggregation-induced emission molecule TPE onto IAPP, allowing real-time monitoring of IAPP oligomer formation and potential application in the diagnosis of T2D.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Aristeidis Papagiannopoulos, Aggeliki Sklapani, Nikolaos Spiliopoulos
Summary: This study presents a method for preparing Hb-based nanoparticles (NPs) using a fully biocompatible approach. These NPs have a spherical structure with a diameter ranging from 50 to 100 nm, and can form electrostatic complexes with CS at pH 4. The NPs can be pH-tunable and stable in solutions with high salt content, making them suitable for nanodelivery of nutrients and drugs.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Andrey V. Struts, Alexander V. Barmasov, Steven D. E. Fried, Kushani S. K. Hewage, Suchithranga M. D. C. Perera, Michael F. Brown
Summary: This article summarizes and reviews the osmotic stress studies of G-protein-coupled receptor rhodopsin. It is found that water plays an important role in the activation of the receptor, with at least 80 water molecules entering the receptor in the transition to the active state. If water influx is prevented, the functional transition of the receptor is reversed. These findings reveal the phenomenon of solvent swelling in the activation mechanism of rhodopsin, with water acting as an allosteric modulator of function for rhodopsin-like receptors in lipid membranes.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Maria Chiara Saija, Adela Melcrova, Wojciech Pajerski, Itay Schachter, Matti Javanainen, Marek Cebecauer, Lukasz Cwiklik
Summary: We used molecular dynamics simulations to investigate the effects of palmitoylation on a transmembrane peptide in different lipid environments. The study found that palmitoylation reduces the peptide's impact on membrane thickness, particularly in lipid-ordered and boundary environments. The hydrophobic palmitoyl chains on the peptide did not significantly affect membrane hydration. Interestingly, the boundary membrane environment was found to be highly compatible with the palmitoylated peptide. These findings have important implications for understanding cell signaling, membrane organization, and optimizing lipid membrane-based drug delivery systems.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Achanta Rishisree, Brayer Mallory, Karnaukhova Elena, Jankovic Teodora, Zdunic Gordana, Savikin Katarina, Jeremic Aleksandar
Summary: Pomegranate peel, ironwort, and chokeberry leaf extracts exhibit anti-aggregative and antitoxic properties against human amylin. They can prevent amyloidosis and cell loss in patients with Type 2 Diabetes Mellitus.
BIOPHYSICAL CHEMISTRY
(2024)