Since its establishment in 2013,BioLiP has become one of the widely used resources for protein-ligand interactions.Nevertheless,several known issues occurred with it over the past decade.For example,the protein-ligand...Since its establishment in 2013,BioLiP has become one of the widely used resources for protein-ligand interactions.Nevertheless,several known issues occurred with it over the past decade.For example,the protein-ligand interactions are represented in the form of single chain-based tertiary structures,which may be inappropriate as many interactions involve multiple protein chains(known as quaternary structures).We sought to address these issues,resulting in Q-BioLiP,a comprehensive resource for quaternary structure-based protein-ligand interactions.The major features of Q-BioLiP include:(1)representing protein structures in the form of quaternary structures rather than single chain-based tertiary structures;(2)pairing DNA/RNA chains properly rather than separation;(3)providing both experimental and predicted binding affinities;(4)retaining both biologically relevant and irrelevant interactions to alleviate the wrong justification of ligands’biological relevance;and(5)developing a new quaternary structure-based algorithm for the modelling of protein-ligand complex structure.With these new features,Q-BioLiP is expected to be a valuable resource for studying biomolecule interactions,including protein-small molecule interaction,protein-metal ion interaction,protein-peptide interaction,protein-protein interaction,protein-DNA/RNA interaction,and RNA-small molecule interaction.Q-BioLiP is freely available at https://yanglab.qd.sdu.edu.cn/Q-BioLiP/.展开更多
A novel carbazole quaternary ammonium compound（abbreviated as T_2） had been synthesized and characterized by ~1H NMR, ^（13）C NMR and Mass spectrometry. The single-crystal structure has been determined by X-ray sin...A novel carbazole quaternary ammonium compound（abbreviated as T_2） had been synthesized and characterized by ~1H NMR, ^（13）C NMR and Mass spectrometry. The single-crystal structure has been determined by X-ray single-crystal diffraction. The electrochemical and two-photon absorption properties of T_2 were systematically studied by cyclic voltammetry and Z-scan determination methods, respectively. The results suggested that T_2 had a good oxidation-reduction and excellent nonlinear optical property. The two-photon absorption（TPA） value has a maximum corresponding to cross section σ = 7963.3 GM（Goeppert-Mayer units） at 700 nm, indicating potential applications in nonlinear optical materials. Furthermore, attributing to the excellent water solubility and low cytotoxicity, the compound was explored on its primary application in biological imaging.展开更多
One organic-decorated quanternaery [TM（1,2-dap）3]Hg Sb2Se5（1,2-dap = 1,2-dianinopropane, TM = Co（1）, Fe（2）） compound has been solvothermally synthesized. The compounds crystallize in triclinic space group P 1,...One organic-decorated quanternaery [TM（1,2-dap）3]Hg Sb2Se5（1,2-dap = 1,2-dianinopropane, TM = Co（1）, Fe（2）） compound has been solvothermally synthesized. The compounds crystallize in triclinic space group P 1, with a = 11.248（6）, b = 11.542（7）, c = 12.180（12） A, V =1268.7（16） A^3, Z = 2, F（000） = 1010 for 1 and a = 11.311（5）, b = 11.558（5）, c = 12.180（9） A, V =1276.5（12） A^3, Z = 2, F（000） = 1008 for 2. The crystal structure consists of one-dimensional anionics chains composed of Hg Se4 tetrahedra and SbSe3 trigonal pyramids sharing corners and[TM（dap）3]^2＋ cations. The [HgSb2Se＋5^2-]∞ anionic chains run along the [001] direction, and are surrounded by the [TM（dap）3]^2＋ cations. Meanwhile, 8-ring [Hg2Sb2Se4] and 6-ring [HgSb2Se2] are alternately found. The compounds were structurally characterized by elemental analysis,thermogravimetric analysis, infrared spectroscopy and UV-Vis diffuse reflectance spectroscopy.展开更多
CONSPECTUS:Peptides and proteins,though both composed of amino acids,differ significantly in their structural and functional complexity.Peptides are generally shorter chains of amino acids and typically adopt simple s...CONSPECTUS:Peptides and proteins,though both composed of amino acids,differ significantly in their structural and functional complexity.Peptides are generally shorter chains of amino acids and typically adopt simple secondary structures,such asα-helices orβ-sheets.However,they rarely develop the intricate tertiary and quaternary structures that are characteristic of proteins.Proteins,which consist of longer polypeptide chains,exhibit complex folding patterns stabilized by various interactions,including hydrogen bonds,disulfide linkages,and hydrophobic interactions.This structural complexity allows proteins to perform highly specialized biological functions,such as enzymatic catalysis,signal transduction,and structural support.Both peptides and proteins have the ability to undergo self-assembly,forming higher-order structures through noncovalent interactions such as hydrogen bonding,electrostatic forces,and hydrophobic interactions.In particular,peptide functional assemblies also serve various roles,such as drug delivery,biosensors,intracellular modulation,and structural scaffolds.Depending on their sequence,they can exhibit antioxidant,antimicrobial,receptor-targeting,or enzyme-inhibitory properties.Peptides also play a crucial role in developing biomaterials like hydrogels and nanomaterials for various applications in both biomedical and engineering fields.Researchers have explored the design of peptide-based hydrogels,nanoparticles,and scaffolds that can mimic extracellular matrices,facilitating cell growth and tissue regeneration.The combination of peptides with other biomaterials has also led to innovative solutions for controlled drug release and antimicrobial coatings.In proteins,self-assembly is crucial for biological function,as exemplified by the formation of multiprotein complexes.These complexes are essential for many biological processes,including structural scaffolds,cellular signaling and immune responses.Among structural protein assemblies,silk has gained significant attention due to its exceptional mechanical properties,biocompatibility,and sustainability.Silk fibers adopt a hierarchical structure comprising crystallineβ-sheet domains interspersed with amorphous regions.This unique arrangement imparts superior strength,elasticity,and toughness,making silk a versatile material for a wide range of applications.Traditionally used in textiles,silk has recently emerged as a promising biomaterial building block in the medical field.Its ability to form various material formats,including fibers,films,and hydrogels,has enabled advancements in drug delivery,wound healing,and regenerative medicine.The expanding field of recombinant silk and peptide engineering holds tremendous promise for sustainable bioengineering and biomaterial development.Advances in synthetic biology and genetic engineering have enabled the mass production of silk-inspired proteins and functional peptides using microbial expression systems.This progress not only reduces reliance on traditional silk production but also expands the possibilities for engineering novel biomaterials with tailored properties.As research in this field continues,the potential applications of silk materials and functional peptides in healthcare,material science,and environmental sustainability are expected to grow,paving the way for groundbreaking innovations in biotechnology and medicine.展开更多
基金supported in part by the National Natural Science Foundation of China(Grant Nos.T2225007 and T2222012)the Foundation for Innovative Research Groups of State Key Laboratory of Microbial Technology,China(Grant No.WZCX2021-03).
文摘Since its establishment in 2013,BioLiP has become one of the widely used resources for protein-ligand interactions.Nevertheless,several known issues occurred with it over the past decade.For example,the protein-ligand interactions are represented in the form of single chain-based tertiary structures,which may be inappropriate as many interactions involve multiple protein chains(known as quaternary structures).We sought to address these issues,resulting in Q-BioLiP,a comprehensive resource for quaternary structure-based protein-ligand interactions.The major features of Q-BioLiP include:(1)representing protein structures in the form of quaternary structures rather than single chain-based tertiary structures;(2)pairing DNA/RNA chains properly rather than separation;(3)providing both experimental and predicted binding affinities;(4)retaining both biologically relevant and irrelevant interactions to alleviate the wrong justification of ligands’biological relevance;and(5)developing a new quaternary structure-based algorithm for the modelling of protein-ligand complex structure.With these new features,Q-BioLiP is expected to be a valuable resource for studying biomolecule interactions,including protein-small molecule interaction,protein-metal ion interaction,protein-peptide interaction,protein-protein interaction,protein-DNA/RNA interaction,and RNA-small molecule interaction.Q-BioLiP is freely available at https://yanglab.qd.sdu.edu.cn/Q-BioLiP/.
基金Supported by the National Natural Science Foundation of China(21271004,51372003,21271003,51432001,21101001)the Natural Science Foundation of Anhui Province(1308085MB24)Scientific Innovation Team Foundation of Educational Commission of Anhui Province(KJ2012A025,2006KJ007TD)
文摘A novel carbazole quaternary ammonium compound（abbreviated as T_2） had been synthesized and characterized by ~1H NMR, ^（13）C NMR and Mass spectrometry. The single-crystal structure has been determined by X-ray single-crystal diffraction. The electrochemical and two-photon absorption properties of T_2 were systematically studied by cyclic voltammetry and Z-scan determination methods, respectively. The results suggested that T_2 had a good oxidation-reduction and excellent nonlinear optical property. The two-photon absorption（TPA） value has a maximum corresponding to cross section σ = 7963.3 GM（Goeppert-Mayer units） at 700 nm, indicating potential applications in nonlinear optical materials. Furthermore, attributing to the excellent water solubility and low cytotoxicity, the compound was explored on its primary application in biological imaging.
基金supported by the National Natural Science Foundation of China(No.21461019)
文摘One organic-decorated quanternaery [TM（1,2-dap）3]Hg Sb2Se5（1,2-dap = 1,2-dianinopropane, TM = Co（1）, Fe（2）） compound has been solvothermally synthesized. The compounds crystallize in triclinic space group P 1, with a = 11.248（6）, b = 11.542（7）, c = 12.180（12） A, V =1268.7（16） A^3, Z = 2, F（000） = 1010 for 1 and a = 11.311（5）, b = 11.558（5）, c = 12.180（9） A, V =1276.5（12） A^3, Z = 2, F（000） = 1008 for 2. The crystal structure consists of one-dimensional anionics chains composed of Hg Se4 tetrahedra and SbSe3 trigonal pyramids sharing corners and[TM（dap）3]^2＋ cations. The [HgSb2Se＋5^2-]∞ anionic chains run along the [001] direction, and are surrounded by the [TM（dap）3]^2＋ cations. Meanwhile, 8-ring [Hg2Sb2Se4] and 6-ring [HgSb2Se2] are alternately found. The compounds were structurally characterized by elemental analysis,thermogravimetric analysis, infrared spectroscopy and UV-Vis diffuse reflectance spectroscopy.
基金supported by the Cabinet Office,Impulsing Paradigm Change through Disrupt Technologies Program(ImPACT)(K.N.)Japan Science and Technology(JST)ERATO(Grant No.JPMJER1602)(K.N.)+3 种基金Grant-in-Aid for Transformative Research Areas(B)(Grant No.JP20H05735)(K.N.)JST COI-Next(Grant Number JPMJPF2114)(K.N.)the MEXT Program:Data Creation and Utilization-Type Material Research and Development Project(Grant Number JPMXP1122714694)(K.N.)JSPS KAKENHI(Grant Number 24K17831)(S.S.Y.L).
文摘CONSPECTUS:Peptides and proteins,though both composed of amino acids,differ significantly in their structural and functional complexity.Peptides are generally shorter chains of amino acids and typically adopt simple secondary structures,such asα-helices orβ-sheets.However,they rarely develop the intricate tertiary and quaternary structures that are characteristic of proteins.Proteins,which consist of longer polypeptide chains,exhibit complex folding patterns stabilized by various interactions,including hydrogen bonds,disulfide linkages,and hydrophobic interactions.This structural complexity allows proteins to perform highly specialized biological functions,such as enzymatic catalysis,signal transduction,and structural support.Both peptides and proteins have the ability to undergo self-assembly,forming higher-order structures through noncovalent interactions such as hydrogen bonding,electrostatic forces,and hydrophobic interactions.In particular,peptide functional assemblies also serve various roles,such as drug delivery,biosensors,intracellular modulation,and structural scaffolds.Depending on their sequence,they can exhibit antioxidant,antimicrobial,receptor-targeting,or enzyme-inhibitory properties.Peptides also play a crucial role in developing biomaterials like hydrogels and nanomaterials for various applications in both biomedical and engineering fields.Researchers have explored the design of peptide-based hydrogels,nanoparticles,and scaffolds that can mimic extracellular matrices,facilitating cell growth and tissue regeneration.The combination of peptides with other biomaterials has also led to innovative solutions for controlled drug release and antimicrobial coatings.In proteins,self-assembly is crucial for biological function,as exemplified by the formation of multiprotein complexes.These complexes are essential for many biological processes,including structural scaffolds,cellular signaling and immune responses.Among structural protein assemblies,silk has gained significant attention due to its exceptional mechanical properties,biocompatibility,and sustainability.Silk fibers adopt a hierarchical structure comprising crystallineβ-sheet domains interspersed with amorphous regions.This unique arrangement imparts superior strength,elasticity,and toughness,making silk a versatile material for a wide range of applications.Traditionally used in textiles,silk has recently emerged as a promising biomaterial building block in the medical field.Its ability to form various material formats,including fibers,films,and hydrogels,has enabled advancements in drug delivery,wound healing,and regenerative medicine.The expanding field of recombinant silk and peptide engineering holds tremendous promise for sustainable bioengineering and biomaterial development.Advances in synthetic biology and genetic engineering have enabled the mass production of silk-inspired proteins and functional peptides using microbial expression systems.This progress not only reduces reliance on traditional silk production but also expands the possibilities for engineering novel biomaterials with tailored properties.As research in this field continues,the potential applications of silk materials and functional peptides in healthcare,material science,and environmental sustainability are expected to grow,paving the way for groundbreaking innovations in biotechnology and medicine.
