髓鞘碱性蛋白对细胞膜脂质分子DPPC、DPPE单层膜影响机理研究

本文通过Langmuir单层膜的表面压力-平均分子面积(π-A)曲线的测定与分析,分别对髓鞘碱性蛋白(MBP)与细胞膜中不同头部基团脂质分子二棕榈酰基磷脂胆碱(DPPC)和二棕榈酰基磷脂酰乙醇胺(DPPE)在空气/液体界面上的相互作用过程进行了系统研究.实验结果表明:(1)当界面上脂质含量一定时,亚相中随着MBP浓度的增大,DPPC、DPPE单层膜的等温线向平均分子面积较大的方向移动;(2)在单层膜表面压力为10 mN/m时,一个MBP分子分别结合140±3个DPPC分子和100±3个DPPE分子,随着表面压力增大,当MBP分子分别与两种磷脂分子相互作用时,MBP插入到磷脂单层界面的个数逐渐减少;(3)随着蛋白质浓度的增加,脂分子形成的单层膜变得较为疏松,且MBP分子易于插入到分子头部较小的DPPE单层膜中;(4)蛋白质的存在使DPPC单层膜的表面压力逐渐减小,且蛋白质浓度越大表面压力降低越多,DPPC被MBP带入到亚相中越多;(5)对于DPPE单层膜,蛋白质通过与DPPE相互作用插入到界面膜中,引起表面压力增大,且蛋白质浓度越高,压力变化量越大.     

Interaction of bovine myelin basic protein with triphosphoinositide

Despite the essential role played by myelin basic protein (MBP) in stabilizing the multilamellar structure of the myelin membrane, attempts at deciphering the structure of MPB have so far failed. Given that MBP is known to specifically interact with the membrane's lipid components, this study was designed to explore the effects of these lipids on the conformation of the protein by examining its interaction with the lipid triphosphoinositide (TPI). MBP was identified by high-performance liquid chromatography (HPLC) in myelin extracted from cow's brain and its molecular weight determined. In aqueous solution, MBP showed a random coil structure confirmed by its circular dichroism (CD) spectra. Possible structural changes to the protein induced by different proportions of TPI were also explored. The CD spectra of these mixtures indicated that this lipid fails to induce the adoption of a secondary structure by MBP. We then performed monolayer experiments to evaluate the type of interaction that occurs between MBP and TPI. First, the molecular weight of the protein sample was established to determine the state of the MBP within the monolayer by applying the equation for gases to the so-called gaseous zone of the monolayer for the conditions under which the expression holds. The similar molecular weights yielded by HPLC performed on dissolved samples and by the monolayers suggests that, as in solution, in the membrane the protein exists as a monomer. Monolayer data suggest forces of attraction between the two components and, through thermodynamic calculations, it was established that this interaction is spontaneous and the interaction is of the electrostatic type.     

Lateral reorganization of myelin lipid domains by myelin basic protein studied at the air-water interface

It has been speculated that adsorption of myelin basic protein (MBP) to the myelin lipid membrane leads to lateral reorganization of the lipid molecules within the myelin membrane. This hypothesis was tested in this study by surface pressure measurement and fluorescent imaging of a monolayer composed of a myelin lipid mixture. The properties of the lipid monolayer before and after addition of MBP into the subphase were monitored. Upon addition of MBP to the monolayer subphase, the surface pressure rose and significant rearrangement of the lipid domains was observed. These results suggest that binding and partial insertion of MBP into the lipid monolayer led to dramatic rearrangement and morphological changes of the lipid domains. A model of adsorption of MBP to the lipid domains and subsequent domain fusion promoted by minimization of electrostatic repulsion between the domains was proposed to account for the experimental observations. The significance of these results in light of the role of MBP in maintaining the myelin structural integrity is discussed.     

桑蚕丝素-RGD融合蛋白的固态结构及其细胞粘附性分析

利用基因工程方法把含有短肽RGD的氨基酸序列连接到桑蚕丝素蛋白的结晶序列GAGAGS上, 通过调节DNA的聚合度, 合成了具有[TGRGDSPA(GVPGV)₂GG(GAGAGS)₃AS]_n一级结构、不同分子量大小的桑蚕丝素-RGD融合蛋白, 并且通过在M9培养基中添加[3-¹³C]Ala的方法进行融合蛋白的稳定同位素标记. ¹³C CP/MAS NMR结果显示, 融合蛋白中的GAGAGS部分具有与天然桑蚕丝素结晶部分相同的分子结构, 即Silk I处理后为均一的分子结构, 而Silk II处理后为不均一的分子结构, 它包含了三种不同的结构成分. 另一方面, 通过对小鼠成纤维细胞BALB/3T3在不同蛋白材料载体上的粘附和增殖性能的测定结果显示, 融合蛋白对细胞的增殖性能与天然胶原蛋白相近, 但表现出了比胶原蛋白更好的细胞粘附性能. 该研究结果显示, 如果对该桑蚕丝素-RGD融合蛋白进行适当加工, 可能适合于组织工程支架材料的应用.     

Molecular dynamics simulation of Matrix Metalloproteinase 2: fluctuations and time evolution of recognition pockets

We report a molecular dynamics simulation study of a zinc-protease--gelatinase A or MMP2--which is a major target for drug design, being involved in tumor metastasis and other degenerative diseases. Two structures have been employed as starting conditions, one based on the crystal of multi-domain proMMP2, the other consisting of the catalytic domain only. The overall fold of the two models is maintained over the 1260 ps trajectory, enabling us to analyze correlations of fluctuations among domains, and to observe the presence of correlations within the catalytic domain in the multi-domain enzyme only, hence due to the presence of hemopexin and fibronectin domains. In the multi-domain protein, two cavities are conserved over the trajectory, one of them pointing to a key region, a crevice surrounding the catalytic zinc. The other one is localized across the three domains of the MMP2 metalloproteinase. These areas are partially covered by the propeptide in the crystal structure of proMMP2. We propose a model of MMP2-collagen interaction that involves both identified cavities and takes into account the inter/intra domain cross-correlations.     

Synthesis and X-ray Crystal Structure of a New Molecular Clip

The synthesis and X-ray crystal structure of a new molecular clip 2 was reported. It （C24H24N4O2, Mr = 400.47） crystallizes in the space group C2/c with a = 15.587（2）, b = 8.5805（12）, c = 15.259（2） A, β = 102.448（3）°, V= 1992.9 （5）A63, Z = 4, Dc = 1.335 g/cm63,μ = 0.087 mm^-1 and F（000） = 848. It remains monomeric in the crystal and a tape-like structure is formed in the crystal structure of molecular clip. The most unusual structural feature of 2 is the boat conformation of its cyclohexyl ring imposed by the ring fusion at C（9）-C（9a）.     

The Molecular Basis of the Interaction of Cyclophilin A with α‐Synuclein

Peptidylprolyl isomerases (PPIases) catalyze cis/trans isomerization of prolines. The PPIase CypA colocalizes with the Parkinson's disease (PD)‐associated protein α‐synuclein in cells and interacts with α‐synuclein oligomers. Herein, we describe atomic insights into the molecular details of the α‐synuclein/CypA interaction. NMR spectroscopy shows that CypA catalyzes isomerization of proline 128 in the C‐terminal domain of α‐synuclein. Strikingly, we reveal a second CypA‐binding site formed by the hydrophobic sequence ⁴⁷GVVHGVATVA⁵⁶, termed PreNAC. The 1.38 Å crystal structure of the CypA/PreNAC complex displays a contact between alanine 53 of α‐synuclein and glutamine 111 in the catalytic pocket of CypA. Mutation of alanine 53 to glutamate, as found in patients with early‐onset PD, weakens the interaction of α‐synuclein with CypA. Our study provides high‐resolution insights into the structure of the PD‐associated protein α‐synuclein in complex with the most abundant cellular cyclophilin.     

Stereoselective synthesis of (3-aminodecahydro-1,4-methanonaphthalen-2-yl)methanols targeted to the C1 domain of protein kinase C

Protein kinase C (PKC) is a widely studied molecular target for the treatment of cancer and other diseases. We have approached the issue of modifying PKC function by targeting the C1 domain in the regulatory region of the enzyme. By using the X-ray crystal structure of the PKCδ C1b domain combined with molecular modeling, we discovered (3-aminodecahydro-1,4-methanonaphthalen-2-yl)methanol as a novel C1 domain ligand. The stereoselective synthesis of this tricyclic γ-amino alcohol was based on two successive Diels-Alder reactions to construct the six continuous stereocenters of the key intermediate.     

A genetic approach for controlling the binding and orientation of proteins on nanoparticles

Although silver nanoparticles are excellent surface enhancers for Raman spectroscopy, their use to probe the conformation of large proteins at interfaces has been complicated by the fact that many polypeptides adsorb weakly or with a random orientation to colloidal silver. To address these limitations, we sought to increase binding affinity and control protein orientation by fusing a silver-binding dodecapeptide termed Ag4 to the C-terminus of maltose-binding protein (MBP), a well-characterized model protein with little intrinsic silver binding affinity. Quartz crystal microbalance measurements conducted with the MBP-Ag4 fusion protein revealed that its affinity for silver (Kd approximately 180 nM) was at least 1 order of magnitude higher than a control protein, MBP2, containing a non-silver-specific C-terminal extension. Under our experimental conditions, MBP-Ag4 SERS spectra exhibited 2-4 fold higher signal-to-background relative to MPB2 and contained a number of amino acid-assigned vibrational modes that were either weak or absent in control experiments performed with MBP2. Changes in amino acid-assigned peaks before and after MBP-Ag4 bound maltose were used to assess protein orientation on the surface of silver nanoparticles. The genetic route described here may prove useful to study the orientation of other proteins on a variety of SERS-active surfaces, to improve biosensors performance, and to control functional nanobiomaterials assembly.     

Molecular Modeling of Interactions of the Benzolactam-V8 Modulators with the Cys2 Domain of Protein Kinase Cδ

Molecular modeling of interactions of four 7- or 8-substituted benzolactam-V8 （BLV） molecules with the cys2 activator-binding domain of protein kinase C （PKCδ） was carried out using molecular docking program Autodock. The docked models reveal that the hydroxymethyl group at the C（5） atom of the eight-membered ring of each BLV is bound at the bottom of the binding groove of the cys2 domain of PKCδ The BLV molecules make hydrogen bonds and hydrophobic interactions with PKCδ, which are similar to those in the crystal structure of the cys2 domain of PKCδ in complex with phorbol 13-acetate. BLV-1 does not contain a long side chain that is hydrophobic and necessary for membrane insertion, so that it would not be a potent modulator of PKCδ. The other three BLV molecules have long side chains substituted at C（7） or C（8） atoms, and it was predicted, based on the docking results, that they had the PKCδ-binding affinity in the order of BLV-2〉BLV-4〉BLV-3, and BLV-2 would be a potent activator of PKCδ.     

A New Approach for Titration Calorimetric Data Analysis on the Binding of Magnesium Ion with Myelin Basic Protein

The interaction of the myelin basic protein (MBP) from the bovine central nervous system with divalent magnesium ion was studied by isothermal titration calorimetry at 27 °C in aqueous solution. A simple rapid method for determination of the dissociation binding constants for Mg²⁺-MBP interaction was introduced using the isothermal titration calometric data. The binding isotherm for Mg²⁺-MBP interaction is easily obtained by carrying out a titration calorimetric experiment using only one set of concentrations of MBP. There are two identical independent intrinsic association constants equal to 0.021 μmol⋅L⁻¹ in the first- and second-binding sites, respectively.     

Evaluation of the carbohydrate recognition domain of the bacterial adhesin FimH: Design, synthesis and binding properties of mannoside ligands

Fimbriae are proteinogeneous appendages on the surface of bacteria, which mediate bacterial adhesion to the host cell glycocalyx. The so-called type 1 fimbriae exhibit specificity for alpha-d-mannosides and, therefore, they are assumed to mediate bacterial adhesion via the interaction of a fimbrial lectin and alpha-d-mannosyl residues exposed on the host cell surface. This carbohydrate-specific adhesive protein subunit of type 1 fimbriae has been identified as a protein called FimH. The crystal structure of this lectin is known and, based on this information, the molecular details of the interaction of mannoside ligands and FimH are addressed in this paper. Computer-based docking methods were used to evaluate known ligands as well as to design new ones. Then, a series of new mannosides with extended aglycon was synthesized and tested as inhibitors of type 1 fimbriae-mediated bacterial adhesion in an ELISA. The results obtained were compared to the predictions and findings as delivered by molecular modeling. This study led to an improved understanding of the ligand-receptor interactions under investigation.     

Thermodynamic Study of Myelin Basic Protein upon Interaction with [Hg2+] Using Extension Solvation Model

Mercury ion interaction with myelin basic protein (MBP) was studied at 300 K in 30 mmol/L tris buffer, pH=7 by isothermal titration calorimetry (ITC). An extended solvation model was used for Hg²⁺+MBP interaction over the whole range of Hg²⁺ concentrations. The binding parameters recovered from the solvation model were attributed to the structural changes of MBP due to its interaction with mercury ion. It was found that mercury ion acted as a noncooperative effector of MBP, and there is a set of two identical and independent binding sites for Hg²⁺ ions. The dissociation equilibrium constant is 97.6 µmol/L. The molar enthalpy change of binding is ?11.25 kJ·mol^?1.     

Domain manipulation of ferroelectric BaTiO3 thin films: application to the local reorientation of liquid crystal

A method is reported for local alignment of nematic liquid crystal (NLC) molecules. It consists in the poling of small areas of ferroelectric thin films using scanning probe microscopy. A liquid crystal deposited onto such a surface is aligned via a dipole-dipole interaction. The ferroelectric films are first characterized using X ray diffraction, atomic force microscopy and ellipsometry. The domain manipulation and local poling of the film are achieved and characterized using an electrostatic microscopy type set-up. A hybrid nematic liquid crystal cell (NLC-OFC: nematic liquid crystal - oxide ferroelectric cell) is then constructed and its alignment inspected using polarizing microscopy (in reflection mode). The reorientation is explained by invoking a simple interaction between the dipole moment of the LC and the surface electric field generated by the poled area. In addition, a complimentary experiment is performed to determine the depth to which the poled area affects the liquid crystal alignment. This consists of measuring the deflection of a collimated beam (optical soliton) propagating across the poled area.     

An Unusual Protein–Protein Interaction through Coupled Unfolding and Binding

Aptides, a novel class of high‐affinity peptides, recognize diverse molecular targets with high affinity and specificity. The solution structure of the aptide APT specifically bound to fibronectin extradomain B (EDB), which represents an unusual protein–protein interaction that involves coupled unfolding and binding, is reported. APT binding is accompanied by unfolding of the C‐terminal β strand of EDB, thereby permitting APT to interact with the freshly exposed hydrophobic interior surfaces of EDB. The β‐hairpin scaffold of APT drives the interaction by a β‐strand displacement mechanism, such that an intramolecular β sheet is replaced by an intermolecular β sheet. The unfolding of EDB perturbs the tight domain association between EDB and FN8 of fibronectin, thus highlighting its potential use as a scaffold that switches between stretched and bent conformations.     

高压下C60晶体玻璃化行为的理论研究

通过构造C_(60)分子间的相互作用，研究了在不同压力下C_(60)晶体中的取向有序结构．利用计算出来的两个取向之间的能量差和相隔势驿，研究了热平衡时取向占有几率和玻璃化转变温度的压力相关性．结果与实验符合．     

In Silico Discovery of Antimicrobial Peptides as an Alternative to Control SARS-CoV-2

A serious pandemic has been caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The interaction between spike surface viral protein (Sgp) and the angiotensin-converting enzyme 2 (ACE2) cellular receptor is essential to understand the SARS-CoV-2 infectivity and pathogenicity. Currently, no drugs are available to treat the infection caused by this coronavirus and the use of antimicrobial peptides (AMPs) may be a promising alternative therapeutic strategy to control SARS-CoV-2. In this study, we investigated the in silico interaction of AMPs with viral structural proteins and host cell receptors. We screened the antimicrobial peptide database (APD3) and selected 15 peptides based on their physicochemical and antiviral properties. The interactions of AMPs with Sgp and ACE2 were performed by docking analysis. The results revealed that two amphibian AMPs, caerin 1.6 and caerin 1.10, had the highest affinity for Sgp proteins while interaction with the ACE2 receptor was reduced. The effective AMPs interacted particularly with Arg995 located in the S2 subunits of Sgp, which is key subunit that plays an essential role in viral fusion and entry into the host cell through ACE2. Given these computational findings, new potentially effective AMPs with antiviral properties for SARS-CoV-2 were identified, but they need experimental validation for their therapeutic effectiveness.     

Rapamycin analogs with differential binding specificity permit orthogonal control of protein activity

Controlling protein dimerization with small molecules has broad application to the study of protein function. Rapamycin has two binding surfaces: one that binds to FKBP12 and the other to the Frb domain of mTor/FRAP, directing their dimerization. Rapamycin is a potent cell growth inhibitor, but chemical modification of the surface contacting Frb alleviates this effect. Productive interactions with Frb-fused proteins can be restored by mutation of Frb to accommodate the rapamycin analog (a rapalog). We have quantitatively assessed the interaction between rapalogs functionalized at C16 and C20 and a panel of Frb mutants. Several drug-Frb mutant combinations have different and nonoverlapping specificities. These Frb-rapalog partners permit the selective control of different Frb fusion proteins without crossreaction. The orthogonal control of multiple target proteins broadens the capabilities of chemical induction of dimerization to regulate biologic processes.     

Determinants of the Inhibition of DprE1 and CYP2C9 by Antitubercular Thiophenes

Mycobacterium tuberculosis (Mtb) DprE1, an essential isomerase for the biosynthesis of the mycobacterial cell wall, is a validated target for tuberculosis (TB) drug development. Here we report the X‐ray crystal structures of DprE1 and the DprE1 resistant mutant (Y314C) in complexes with TCA1 derivatives to elucidate the molecular basis of their inhibitory activities and an unconventional resistance mechanism, which enabled us to optimize the potency of the analogs. The selected lead compound showed excellent in vitro and in vivo activities, and low risk of toxicity profile except for the inhibition of CYP2C9. A crystal structure of CYP2C9 in complex with a TCA1 analog revealed the similar interaction patterns to the DprE1–TCA1 complex. Guided by the structures, an optimized molecule was generated with differential inhibitory activities against DprE1 and CYP2C9, which provides insights for development of a clinical candidate to treat TB.     

Role of the interaction between forming nanocrystals and glass surface on the structure and properties of ZnO-based films

The interaction between glass surface and forming nanocrystals plays the important role in the formation of thin ZnO coatings crystal structure. The comparative study of the crystal structure of thin ZnO-based films and powders having similar chemical compositions was performed with the use of SEM, XRD analysis, optical, and luminescent spectroscopy. The influence of different coatings parameters (chemical composition, thickness) on the spectroscopic and morphological properties of thin films and powders reveals the structural features of the interaction between forming ZnO nanocrystals and glass surface. ZnO–SnO₂ coatings and powders were prepared by liquid polymer-salt technique. This method provides the close contact between the coatings’ precursors with a surface of the glass during both the nucleation and the initial growth stage of forming oxide crystals. The interaction of nanocrystals and substrate surface is responsible for the texture formation in the ZnO films and determines some features of their optical properties.