The mechanism of HMGB1 secretion and release

High mobility group box 1 (HMGB1) is a nonhistone nuclear protein that has multiple functions according to its subcellular location. In the nucleus, HMGB1 is a DNA chaperone that maintains the structure and function of chromosomes. In the cytoplasm, HMGB1 can promote autophagy by binding to BECN1 protein. After its active secretion or passive release, extracellular HMGB1 usually acts as a damage-associated molecular pattern (DAMP) molecule, regulating inflammation and immune responses through different receptors or direct uptake. The secretion and release of HMGB1 is fine-tuned by a variety of factors, including its posttranslational modification (e.g., acetylation, ADP-ribosylation, phosphorylation, and methylation) and the molecular machinery of cell death (e.g., apoptosis, pyroptosis, necroptosis, alkaliptosis, and ferroptosis). In this minireview, we introduce the basic structure and function of HMGB1 and focus on the regulatory mechanism of HMGB1 secretion and release. Understanding these topics may help us develop new HMGB1-targeted drugs for various conditions, especially inflammatory diseases and tissue damage.Subject terms: Molecular biology, Medical research     

N-glycosylation of High Mobility Group Box 1 protein (HMGB1) modulates the interaction with glycyrrhizin: A molecular modeling study

High Mobility Group Box 1 protein (HMGB1) is an abundant protein with multiple functions in cells, acting as a DNA chaperone and damage-associated molecular pattern molecule. It represents an attractive target for the treatment of inflammatory diseases and cancers. The plant natural product glycyrrhizin (GLR) is a well-characterized ligand of HMGB1 and a drug used to treat diverse liver and skin diseases. The drug is known to bind to each of the two adjacent HMG boxes of the non-glycosylated protein. In cells, HMGB1 is N-glycosylated at three asparagine residues located in boxes A and B, and these N-glycans are essential for the nucleocytoplasmic transport of the protein. But the impact of the N-glycans on drug binding is unknown. Here we have investigated the effect of the N-glycosylation of HMGB1 on its interaction with GLR using molecular modelling, after incorporation of three N-glycans on a Human HMGB1 structure (PDB code 2YRQ). Sialylated bi-antennary N-glycans were introduced on the protein and exposed in a folded or an extended conformation for the drug binding study. The docking of the drug was performed using both 18α- and 18β-epimers of GLR and the conformations and potential energy of interaction (ΔE) of the different drug-protein complexes were compared. The N-glycans do not shield the drug binding sites on boxes A and B but can modulate the drug-protein interaction, via both direct and indirect effects. The calculations indicate that binding of 18α/β-GLR to the HMG box is generally reduced when the protein is N-glycosylated vs. the non-glycosylated protein. In particular, the N-glycans in an extended configuration significantly weaken the binding of GLR to box-B. The effects of the N-glycans are mostly indirect, but in one case a direct contact with the drug, via a carbohydrate-carbohydrate interaction, was observed with 18β-GLR bound to Box-B of glycosylated HMGB1. For the first time, it is shown (at least in silico) that N-glycosylation, one of the many post-translational modifications of HMGB1, can affect drug binding.     

Structural feature of bent DNA recognized by HMGB1

High Mobility Group Box 1 (HMGB1) protein, a potential therapeutic target, binds bent DNAs structure-specifically. Here we report on a crucial structural feature of the bent DNA required for strong binding to HMGB1. NMR structures of two bent DNA oligomers, only one of which binds strongly to HMGB1, revealed that the presence of a pocket structure on the minor groove is crucial for strong binding through penetration of a phenylalanine residue.     

Recognition determinants in a T4 ← G4 mutant derived from a 5′-GCGTGGGCGT-3′ oligomer in a zinc finger 268–DNA complex.

The 5′-GCGTGGGCGT-3′ (T4) oligomer found in the zinc finger 268–DNA complex was mutated into the sequence 5′-GCGGGGGCGT-3′ (G4). A 3D model was constructed from the T4 sequence using an X-ray structure as a template. Molecular dynamics simulations were used to test the thermal stability of the model. A 500-ps trajectory was obtained for the fully charged complex in water using GROMOS87. The complex and the G4 sequence are found to have dynamically stationary behavior. Comparisons made with a previous T4 sequence molecular dynamics simulation show both systems have similar thermal stability. The structure of DNA appears to be maintained by its global interactions with the protein although the mutated site does not contribute with its full potential for binding. The protein structure shows some small differences compared to the T4 simulation. The simulation provided evidence for the role of a chloride ion interacting with the protein and helping in the recognition process. Received: 21 June 1999 / Accepted: 19 October 1999 / Published online: 14 March 2000     

Modelling radiation-induced damage in the lac operator –lac repressor complex. DNA damage: 8-oxoguanine

 Among the DNA lesions induced by ionising radiation, one of the most abundant base modifications is that of guanine (G) into 8-oxo-7-hydro-2′-deoxyguanosine (oxoG). The Escherichia coli lac operator–lac repressor complex bearing one or several oxoG was studied by molecular modelling. The initial structure of the complex was obtained from the Protein Data Bank (1CJG entry – model 1). Systematic replacements of G by oxoG were carried out. Modelling involved energy-minimisation and simulated-annealing techniques using the Amber force field. Depending on its location along the DNA sequence, oxoG induces modifications of the energetic characteristics of the complex, the electrostatic potential distribution on the surfaces of the DNA and of the protein, the DNA and protein conformations and DNA and protein flexibility. In the case of the replacement of G by oxoG at position 8 of the fragment, the most noticeable effects are a 13% decrease in the interaction energy and a 14% reduction in the number of intermolecular hydrogen bonds, all other effects being much weaker. Therefore, we may conclude that the presence of one or several such base modifications is insufficient to account, alone, for the experimental observation of the radiation-induced decrease of lac operator–lac repressor binding extent. Received: 20 July 2000 / Accepted: 5 January 2001 / Published online: 3 April 2001     

Interaction of fumigaclavine C with High Mobility Group Box 1 protein (HMGB1) and its DNA complex: A computational approach

The fumigaclavines represent a small group of clavine-type alkaloids produced by the pathogenic fungus Aspergillus fumigatus. The leading compound in the family is fumigaclavine C (Fm-C) endowed with potent anti-inflammatory properties. Fm-C represses the production of several inflammatory cytokines in cells via a mechanism implicating a reduced nucleo-cytoplasmic transport and extracellular export of the alarmin protein HMGB1, through a direct drug-protein interaction, and a down-regulation of HMGB1 expression. We have investigated the interaction of Fm-C with HMGB1 using two complementary forms of the HMG-box protein, in its free and DNA-bound configurations, using molecular modeling. We identified up to six potential binding sites for Fm-C in the vicinity of the B-box of HMGB1, with the site designated Lys-103 being the most favored and maintained when the protein is bound to a 16-base pair DNA oligonucleotide. Structure-binding relationships have been explored through the comparison of the HMGB1-binding properties of fumigaclavines A, B and C, and the related alkaloid lysergic acid diethylamide (LSD). Both the C-9 acetyl group and C-2 dimethylallyl side chain of Fm-C contribute importantly to the protein interaction. LSD appears also to form stable complexes with free HMGB1. According to the calculated empirical energies of interaction (ΔE), the compounds rank in the order: Fm-C ∼ LSD < Fm-A < Fm-B, for binding to HMGB1. The study helps to better comprehend the mechanism of action of Fm-C, and its anti-inflammatory and anticancer properties.     

4-氯-2-(1H-咪唑并[4,5-f][1,10]菲咯啉)苯酚铜(Ⅱ)配合物的晶体结构及其与DNA的相互作用

利用菲咯啉酮衍生物4-氯-2-(1H-咪唑并[4,5-f][1,10]菲咯啉)苯酚(HL)设计合成了一种新的单核铜配合物[Cu(L)(5-Cl-sal)(DMF)]ClO_4·DMF(5-Cl-Hsal=5-氯-水杨醛),用元素分析和X射线单晶衍射等手段对配合物进行了表征。该配合物晶体属三斜晶系,P1空间群。用紫外吸收光谱、荧光光谱和凝胶电泳等方法研究了配合物与DNA的相互作用。结果表明,配合物以插入方式与CT-DNA结合,结合常数为1.02×10~3 L·mol~(-1)。同时配合物也能较大程度淬灭EB-DNA复合物的荧光,表观键合常数为4.37×10~5L·mol_(-1),略小于经典键合常数107 L·mol~(-1)。淬灭机理为动态淬灭。凝胶电泳实验研究表明配合物在H_2O_2存在下可将pBR322质粒DNA切割为开环缺口型DNA和线型DNA,配合物浓度越大,切割效果越好。机理研究显示,配合物切割DNA的反应是由羟基自由基(·OH)和单线态氧(~1O_2)作为活性物种的氧化切割过程。     

Molecular modeling and spectroscopic studies on the binding of guaiacol to human immunoglobulin

The fluorogenic property of guaiacol was exploited for the first time to analyze the interaction with target protein as a probe by molecular modeling, fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. Molecular docking was performed to reveal the possible binding mode or mechanism and suggested that guaiacol can strongly bind to human immu- noglobulin (HIgG). It is considered that guaiacol binds to HIgG mainly by a hydrophobic interaction and there are two hydrogen bond interactions between the drug and the residues LEU 80 and ASP 65, which is in good agreement with the results from the experimental thermodynamic parameters (the enthalpy change △H0 and the entropy change △S0 were calculated to be 65.55 kJ·mol-1 and 132.95 J·mol-1·K-1 according to the Vant’ Hoff equation). Data obtained by the fluorescence spectroscopy indicated that binding of guaiacol with HIgG leads to dramatic enhancement in the fluorescence emission intensity along with significant occurrence of efficient Frster resonance energy transfer (FRET) from the residue of HIgG to the protein bound guaiacol. From the low value of fluorescence anisotropy (r = 0.06), it is argued that the probe molecule is located in the motionally unrestricted environment of the protein. The alterations of protein’s secondary structure in the presence of guaiacol in aqueous solution were quantitatively calculated by the evidences from FT-IR and CD spectroscopes.     

Crystal structure and DNA interaction of a nickel(II) complex with N-benzyl-N ′-[2-(benzylamino)ethyl]ethane-1,2-diamine

N-Benzyl-N′-[2-(benzylamino)ethyl]ethane-1,2-diamine was prepared by reduction of its Schiff base analog. Its Ni(II) complex was synthesized and characterized. The crystal structure of the complex showed a square pyramidal structure in which a chlorine atom bridges two Ni(II) atoms in the common apical position. The dinuclear complex has two identical five-coordinate Ni(II) atoms. Interaction of the complex with calf thymus DNA was investigated by UV spectroscopy and fluorescence spectroscopy, and the results suggest that the complex binds to DNA by electrostatic interactions only. The binding constant is 1.02 × 10⁴ mol⁻¹ L.     

Study on the binding of puerarin to bovine serum albumin by isothermal titration calorimetry and spectroscopic approaches

The interaction of a flavonoid molecule (puerarin) with bovine serum albumin (BSA) was characterized by isothermal titration calorimetry (ITC), optical spectroscopic technique, and molecular modeling method under physiological conditions. The binding parameters for the reaction were calculated according to ITC experiments at different temperatures. The thermodynamic parameters, negative enthalpy changes (ΔH), and positive entropy (ΔS) indicated that the binding processes were entropically driven. The alterations of protein secondary structure in the presence of puerarin in aqueous solution were estimated by the evidences from FT-IR and CD spectroscopy with reductions of α-helices. On the basis of fluorescence resonance energy transfer (FRET) between excited tryptophan in BSA and BSA bound puerarin, the critical transfer distance and mean distance between tryptophan in BSA and puerarin were estimated.     

4-氯-2-(1H-咪唑并[4,5-f][1,10]菲咯啉)苯酚铜(Ⅱ)配合物的晶体结构及其与DNA的相互作用

利用菲咯啉酮衍生物4-氯-2-(1H-咪唑并[4,5-f][1,10]菲咯啉)苯酚(HL)设计合成了一种新的单核铜配合物[Cu (L)(5-Cl-sal)(DMF)]ClO₄·DMF (5-Cl-Hsal=5-氯-水杨醛),用元素分析和X射线单晶衍射等手段对配合物进行了表征。该配合物晶体属三斜晶系,P1空间群。用紫外吸收光谱、荧光光谱和凝胶电泳等方法研究了配合物与DNA的相互作用。结果表明,配合物以插入方式与CT-DNA结合,结合常数为1.02×10³ L·mol^-1。同时配合物也能较大程度淬灭EB-DNA复合物的荧光,表观键合常数为4.37×10⁵ L·mol^-1,略小于经典键合常数10⁷ L·mol^-1。淬灭机理为动态淬灭。凝胶电泳实验研究表明配合物在H₂O₂存在下可将pBR322质粒DNA切割为开环缺口型DNA和线型DNA,配合物浓度越大,切割效果越好。机理研究显示,配合物切割DNA的反应是由羟基自由基(·OH)和单线态氧(¹O₂)作为活性物种的氧化切割过程。     

Theoretical study for quercetin/β-cyclodextrin complexes: quantum chemical calculations based on the PM3 and ONIOM2 method

The inclusion interaction between quercetin and β-cyclodextrin (β-CD) binding site has been investigated, based on PM3 and ONIOM2 methods. The obtained results clearly indicate that the orientation in which the B ring of the guest molecule located near the secondary hydroxyls of the β-CD cavity is preferred in the binding energy. Moreover, Analyses regarding the complex structures suggest that one hydrogen bond between 7-hydroxy group (OH) of quercetin and 6-OH of β-CD is formed. This hydrogen bond interaction plays an important role in the bound quercetin/β-CD complex.     

Inclusion Complex Formation Between Modified Cyclodextrins and Riboflvin and Alloxazine in Aqueous Solution

Inclusion complex formation of hydroxypropylated α-, β- and γ-cyclodextrins with riboflavin (vitamin B₂) and alloxazine was studied by spectroscopic and solubility methods. Alloxazine, which is a structural analog of riboflavin, was considered in order to evaluate the role of ribityl and methyl substituents in complexation. Thermodynamic parameters for 1:1 complex formation were obtained and analyzed in terms of influence of the reagent structure on the binding process. It was shown that the cavity of hydroxypropyl-β-cyclodextrin is more appropriate for formation of stable complexes. The complexes are enthalpy stabilized, due to prevalence of van der Waals interactions and possible hydrogen bonding. The partial insertion of riboflavin into the cyclodextrin cavity was revealed by ¹H NMR and computer modeling. The ribityl side chain, which prevents deep inclusion, is located nearby the wider rim of the cyclodextrin molecule and can undergo destruction. Penetration of the alloxazine molecule into the macrocyclic cavity is deeper and accompanied by formation of more stable inclusion complexes. Hydroxypropyl-β-cyclodextrin was found to be the more efficient solubilizing agent for riboflavin and alloxazine, whereas a stabilization action of cyclodextrins towards riboflavin was not observed.     

Cyclodextrins Binding to Paeonol and Two of Its Isomers in Aqueous Solution. Isothermal Titration Calorimetry and 1H NMR Investigations of Molecular Recognition

Interactions between CDs with three substituted phenols, paeonol (Pae), acetovanillone (Ace) and 2-hydroxyl-5-methoxy-acetophone (Hma), which are isomers, have been determined by isothermal titration calorimetry (ITC) and ¹H NMR in aqueous solution at 298.2 K. Both the binding thermodynamics and ¹H NMR spectra show that the interaction between α-cyclodextrin (α-CD) molecule and each guest molecule is extremely weak. The thermodynamic parameters indicate that the binding processes of β-cyclodextrin (β-CD) with the isomers are mainly entropy driven and that β-CD binds with Pae or Ace in 1:1 stoichiometry, whereas with Hma binds in 1:1 and 2:1 stoichiometries. The thermodynamic parameters also suggest that γ-cyclodextrin (γ-CD) binds each isomer in the same 1:1 stoichiometry. The binding processes of Pae and Hma with γ-CD are enthalpy driven whereas Ace with γ-CD is predominantly driven by entropy. The ¹H NMR spectra reveal that the three isomers were trapped into the torus cavity of the β-CD molecule from the narrow side during the binding process. Pae penetrates into the γ-CD cavity from the primary rim of the macrocycle whereas Ace does so from the secondary rim, but Hma appears not interact with the internal cavity of γ-CD at all.     

Towards a fluorescent molecular switch for nucleic acid biosensing

A novel fluorescent molecular switch for the detection of nucleic acid hybridization has been explored in relation to the development of a structure that would be amenable for operation when immobilized for solid-phase analyses. The structure was prepared by self-assembly, and used Neutravidin as the central multivalent docking molecule, a newly synthesized biotinylated long-chain linker for intercalating dye that was modified with thiazole orange (TO) at one end, and a biotinylated probe oligonucleotide. Self-assembly of the biotinylated components on adjacent Neutravidin binding sites allowed for physical placement of an oligonucleotide probe molecule next to tethered TO. The TO located at the end of the flexible linker chain was available to intercalate, and could report if a duplex structure was formed by a probe–target interaction by means of fluorescence intensity. Subsequently, regeneration of the single-stranded probe was possible without loss of the intercalator to solution. The switch constructs were assembled in solution and subsequently immobilized onto biotin functionalized optical fibers to complete the sensor design. Solution-phase fluorescence lifetime data showed a biexponential behavior for switch constructs, suggesting intercalation as well as a significant secondary binding mode for the immobilized TO. It was found that the secondary binding mechanism for the dye to DNA could be decreased, thus shifting the dye to intercalative binding modes, by adjusting the solution conditions to a pH below the pI of Neutravidin, and by increasing the ionic strength of the buffer. Preliminary work demonstrated that it was possible to achieve up to a fivefold increase in fluorescence intensity on hybridization to the target.     

Thermodynamic and spectrographic studies on the interactions of ct-DNA with 5-fluorouracil and tegafur

The interactions of calf thymus deoxyribonucleic acid (ct-DNA) with two antitumour drugs (5-fluorouracil and tegafur) in aqueous buffer solution (pH 7.40) have been investigated using nano-watt-scale isothermal titration calorimetry (ITC), circular dichroism (CD), ultraviolet absorption (UV) and fluorescence spectroscopy. Thermodynamic parameters, i.e., binding proportions and constants, standard changes of enthalpy (ΔH°), Gibbs free energy (ΔG°) and entropy (ΔS°) have been derived from the calorimetric data. The binding ratios of 5-fluorouracil and tegafur with base pairs in ct-DNA are 1:3 and 1:4, respectively. The thermodynamic parameters have been discussed according to the influence of drugs on molecular structure of the DNA shown spectrogram. The results indicate that molecule of 5-fluorouracil or tegafur can intercalate itself into the intra-molecular space formed by DNA double helix and cause some changes in the secondary structure of DNA molecule.     

Effect of acetic acid on the adhesion-capillary interaction of an atomic force microscope probe with immunoglobulin G

It is established that the interaction of immunoglobulin G with 1% acetic acid increases the adhesion-capillary interaction between the atomic force microscope probe and immunoglobulin G covalently bound to the surface of the glass more than 2 times. Changes in the Fourier-IR absorption band of the first and second amide bands of immunoglobulin G due to the interaction of protein with 1% acetic acid indicates a change in the secondary structure of protein in favor of the component of β-sheet structure with a peak of 1635 ± 1 cm⁻¹. It is concluded that the probable cause of the change of adhesion-capillary interaction is a change in the secondary structure of proteins.