漆酶与酚类模式底物的结合及反应活性的理论研究

通过生物信息学分析、分子动力学模拟及量子化学计算,对21种邻对位取代酚类模式底物与漆酶的结合能力以及反应活性进行了探讨.生物信息学结构比对分析发现漆酶的活性口袋含有Asp/Glu206,Asn/His208,Asn264,Gly392和His458等保守的氨基酸残基(氨基酸残基编号以Trametes versicolor漆酶为例,PDB:1KYA);采用MM-GBSA方法计算了21种酚类模式底物与T.versicolor漆酶的结合自由能.分子力学计算结果表明,漆酶与底物的结合力主要来自Asp206和Asn264等残基与底物分子形成的分子间氢键,并且Phe265残基和酚类底物的芳香环形成π-π相互作用.量子化学计算表明,芳环上取代基的推拉电子效应显著影响协同电子转移的底物去质子化过程,其中推电子能力较强的—NH2,—OH,—OCH3和—CH CHCH3等基团能够明显增强酚羟基反应活性,而吸电子的—CONH2和—Cl则具有相反的效应.     

化学修饰法表征Bacillus smithii T7产耐热菊粉酶催化活性中心的必需氨基酸残基

采用化学修饰法研究了史氏芽胞杆菌Bacillus smithiiT7产耐热菊粉酶活性中心氨基酸残基,发现该酶活性中心存在一个组氨酸残基和一个谷氨酸(或天冬氨酸)残基.修饰前后的酶动力学参数变化表明组氨酸残基参与了底物的结合和催化过程,而谷氨酸(或天冬氨酸)的羧基亲核攻击促使底物分解.邹氏作图法证明酶活性中心存在两个必需的色氨酸残基,荧光和圆二色光谱研究表明色氨酸残基在酶的催化和酶的耐热性方面起重要作用.     

细胞色素c突变体的共振拉曼光谱研究

采用共振拉曼光谱技术研究了细胞色素c一次突变体（WT）及其突变体Y67F和N52I在低频区的光谱特征。结果表明，以苯丙氨酸替代WT中酪氨酸残基Tyr67并没有明显影响血红素丙氨酸侧基周围多肽氨基酸残基的构象，而异亮氨酸对天冬酰胺残基Asn52的取代则较大程度地改变了蛋白质内部水分子与周围氨基酸残基间的氢键作用和多肽空腔的疏水性，进而使氨基酸残基和血素的构象相应发生调变。两种取代都导致形成血红素周围空腔的多肽氨基酸残基构象的变化。     

CYP2C9酶与Warfarin结合模型的立体选择性理论研究

对CYP2C9酶与S-Warfarin复合物的晶体结构进行分子对接、分子动力学模拟、通道分析及结合自由能计算,发现原晶体结构中的结合模式为"亚稳态",提出了CYP2C9与S-Warfarin结合的可催化模式;比较了CYP2C9与S-和R-Warfarin结合的异同,确定了在结合过程中起重要作用的锚定氨基酸残基,尤其是位于活性位点区域的苯丙氨酸簇.在结合过程中这些残基通过芳香环的移动对稳定底物的结合模式起到至关重要的作用,阐明了该酶呈现相关底物选择性的原因.对于CYP2C9与底物对接模式及立体选择性的研究有助于在分子层面上理解特异性底物与酶的结合特点,为潜在的药物设计提供了合理可信的理论依据.     

基于分子动力学模拟的VmoLac非特异性底物催化活性的理论研究

采用分子动力学模拟方法研究了VmoLac的非特异性底物催化活性, 模拟了VmoLac/3-oxo-C10-AHL, VmoLac/3-oxo-C6-AHL, VmoLac/γ-nonalacton和VmoLac/ethyl-paraoxon 4个复合物. 分析了分子动力学模拟过 程中不同底物结合引起VmoLac构象变化的主要原因. 结果表明, 3-oxo-C10-AHL和γ-nonalacton的结合会使VmoLac活性口袋附近的Loop8结构域运动明显, 利于底物结合在Loop8疏水通道外侧进而引起催化反应; VmoLac活性口袋周围的门控残基W264和Y230之间距离的变化会影响底物的结合; Y98与长链内酯、 壬内酯的羰基碳之间形成的进攻距离较小, 而与短链内酯的羰基碳以及对氧磷的磷原子之间形成的进攻距离较大, 短的距离更有利于发生亲核进攻反应; D257是引发VmoLac催化反应的关键残基; 当VmoLac催化3-oxo-C10-AHL和γ-nonalacton时, D257与极化水以及底物形成更多的氢键, 使底物与酶更容易结合. 从理论催化机制角度解释了VmoLac催化长链内酯(3-oxo-C10-AHL)比短链内酯(3-oxo-C6-AHL)的能力强, 催化壬内酯(γ-nonalacton)比对氧磷(ethyl-paraoxon)能力强的原因, 为实验结果提供了理论证明.     

钴(Ⅱ)-氨基酸配合物催化性能与氧合性能的关系

研究了13种钴(Ⅱ)-氨基酸配合物的可逆氧合性能和催化性能之间的关系,通过配合物活化分子氧(O2)氧化环己烯考察其催化性能.结果表明,13种钴(Ⅱ)-氨基酸配合物均具有不同程度的可逆氧合性能和催化活性.配合物完成一个可逆吸氧周期的用时越短,其可逆氧合性能越好,催化性能越差;相反,吸氧周期长及可逆氧合性能差的配合物其催化性能却更好.另外,在对配合物不同配比的研究中发现,Co(Ⅱ)与氨基酸的摩尔比为1∶3(或1∶2)饱和配位时,可逆吸氧性能较好,但其催化性能较差,环己烯转化率较低;在1∶1型配位不饱和时,吸氧的可逆性较差,但催化性能优良,环己烯的转化率可达82.5%.结合结构分析和理论计算的结果可知,不同钴(Ⅱ)-氨基酸配合物的氧合可逆性和催化性能的差异,主要归因于氨基酸配体的残基与Co(Ⅱ)的结合能力的不同.氨基酸配体的残基与Co(Ⅱ)的结合能力越好,越有利于配合物由高自旋态向低自旋态转化,并与O2可逆结合,不利于烯烃基的取代,配合物表现出较差的催化性能,反之亦然.     

钴(Ⅱ)-氨基酸配合物催化性能与氧合性能的关系

研究了13种钴(Ⅱ)-氨基酸配合物的可逆氧合性能和催化性能之间的关系, 通过配合物活化分子氧(O₂)氧化环己烯考察其催化性能. 结果表明, 13种钴(Ⅱ)-氨基酸配合物均具有不同程度的可逆氧合性能和催化活性. 配合物完成一个可逆吸氧周期的用时越短, 其可逆氧合性能越好, 催化性能越差; 相反, 吸氧周期长及可逆氧合性能差的配合物其催化性能却更好. 另外, 在对配合物不同配比的研究中发现, Co(Ⅱ)与氨基酸的摩尔比为1:3(或1:2)饱和配位时, 可逆吸氧性能较好, 但其催化性能较差, 环己烯转化率较低; 在1:1型配位不饱和时, 吸氧的可逆性较差, 但催化性能优良, 环己烯的转化率可达82.5%. 结合结构分析和理论计算的结果可知, 不同钴(Ⅱ)-氨基酸配合物的氧合可逆性和催化性能的差异, 主要归因于氨基酸配体的残基与Co(Ⅱ)的结合能力的不同. 氨基酸配体的残基与Co(Ⅱ)的结合能力越好, 越有利于配合物由高自旋态向低自旋态转化, 并与O₂可逆结合, 不利于烯烃基的取代, 配合物表现出较差的催化性能, 反之亦然.     

结合分子模拟探讨共聚酯PBSH在不同溶剂中的PC脂肪酶催化降解

采用固定化洋葱假单胞菌(PC)脂肪酶为催化剂,研究了在氯仿和四氢呋喃(THF)中不同摩尔比的聚(丁二酸丁二醇-co-丁二酸己二醇酯)(PBSH)的酶促降解规律及其差异性.通过PBSH降解前后的相对分子质量变化、降解产物的MALDI-TOF-MS分析研究了共聚酯降解规律,并以分子动力学(MD)及分子对接模拟分别研究了PC酶的溶剂效应及酶与底物的结合机制.研究结果表明,PC酶在2种溶剂中均可催化PBSH降解,但在氯仿中酶的活性较大,PBSH降解率大.分子动力学模拟数据表明,在THF中,PC酶整体氨基酸残基的涨落比氯仿中大,且THF会进入酶活性口袋中与催化残基Ser87结合,破坏了催化残基Ser87和His286之间的相互作用.分子对接结果分析发现,含丁二酸己二醇酯(HS)单元底物与PC酶活性位点的对接比含丁二酸丁二醇酯(BS)单元的更为稳定.     

L-乳酸脱氢酶抑制剂抑制成因的探讨

应用HF/3 21G研究了抑制剂H2N－CO－COO－对L 乳酸脱氢酶的抑制成因.结果表明,酶被抑制的主要原因有:(1)抑制剂与底物的稳定构象态在结构上极为相似,导致酶不能有效识别底物;(2)模型抑制剂各原子所带净电荷的优势使抑制剂更易与酶活性中心结合;(3)抑制剂通过对酶的诱导契合作用使酶活性中心的空间被缩小;(4)对活性中心有关结构的分析表明,底物的甲基分子片以及酶的氨基酸残基Gln 102,对催化反应能否顺利进行,影响极大.     

酶结构的网络表征及催化位点的预测

酶是生物体内的一种活性催化剂,通过绑定反应底物降低反应活化能从而高效催化各种生物化学反应.酶催化活性中心由少数氨基酸残基组成,它们直接参与酶反应,包括质子交换、结构的稳定和底物绑定等.尽管越来越多的酶结构已被测定,但现在从结构仍难以确定催化位点.     

Effect of the hyaluronidase microe nvironment on the enzyme structure–function relationship and computational study of the <Emphasis Type="Italic">in silico</Emphasis> molecular docking of chondroitin sulfate and heparin short fragments to hyaluronidase

The review addresses the biochemical interactions of hyaluronidases with components of the natural microenvironment. The effect of subtle structural differences between ligands on the enzyme structure–function relationship regulation is noted. Docking of chondroitin sulfate (CS) trimers (hexasaccharides) and heparin tetramers (octasaccharides) to the 3D model of the bovine testicular hyaluronidase (BTH) was performed by computational chemistry methods in order to elucidate the mechanism of regulation of the enzyme functioning in the body (using virtual screening, molecular dynamics, and calculation of surface electrostatic potential of protein complexes). Several binding sites for glycosaminoglycan (GAG) ligands were found to occur on the hyaluronidase surface. They are identical for CS trimers and heparin tetramers. The calculations showed the possibility of both reversible and irreversible conformational changes of the 3D structure of BTH, depending on the arrangement of negatively charged ligands on its globule. When the changes are irreversible, Glu-149 and Asp-147, which are key amino acid residues for the catalytic activity of BTH, can migrate from the vicinity of the native enzyme active site to the periphery of the protein molecule, thus inducing enzyme inactivation. The interaction of the GAG ligands with the BTH active site is mainly caused by electrostatic forces. Four or five binding sites of the chondroitin sulfate trimer proved to be critical for stabilization of the enzyme structure. Their occupation was sufficient for preventing irreversible deformation of the BTH molecule upon the insertion of the heparin ligand into the active site cavity. Protein stabilization is accompanied by the formation of a particular form of the surface electrostatic potential.     

Modelling the active site of glyceraldehyde-3 phosphate dehydrogenase with the LSCF formalism

In the framework of a theoretical approach to the relationship between structure and reactivity of the catalytic centers of enzymes, glyceraldehyde-3 phosphate dehydrogenase (GAPDH) has been chosen as a model enzyme. In GAPDH, the proximity of His₁₇₆ increases the reactivity of Cys₁₄₉ at neutral pH; however, its presence alone is not sufficient to explain the reactivity of the catalytic Cys. In order to determine which other interactions play an important role, a study of the geometric and electronic structure of the catalytic site has been made using a hybrid quantum mechanics/molecular mechanics local self-consistent field method. This allows the computation of the electronic properties of amino acid residues in subsystems influenced by other parts of the macromolecule. The quantum subsystem was centered on the Cys₁₄₉ residue of GAPDH. The structures of GAPDH taken from the crystallographic database did not include hydrogen atoms and these had to be added taking into account the fact that, in the active site, His₁₇₆ has three tautomeric forms: δ-His protonated, ε-His protonated and His⁺. The results presented here suggest that the most stable His…Cys system in GAPDH is a strongly hydrogen-bonded Cys₁₄₉ ⁻/His₁₇₆ ⁺ ion pair. Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 23 November 1998     

Site-selective labeling strategies for screening by NMR

NMR based screening has become an important tool in the pharmaceutical industry. Methods that provide information on the location of small molecule binding sites on the surface of a drug target (e. g. SAR-by-NMR and related techniques) are of particular interest. In order to extend the applicability of such techniques to drug targets of higher molecular weight, selective labeling strategies may be employed. Dual-amino acid selective labeling and site directed non-native amino acid replacement (SNAAR) allow for the selective detection of NMR resonances of a specific amino acid residue. This results in significantly reduced spectral complexity, which not only enables application to higher molecular weight systems, but also eliminates the need for sequential resonance assignment in order to identify the binding site. Regio-selective (or segmental) labeling of an entire protein domain of a multi domain protein may also be achieved. Labeling only a selected part of a multi domain protein (e. g. a catalytic or ligand binding domain) is an attractive way to simplify the spectral interpretation without disturbing the system under study.     

离子液体的量化计算及分子动力学模拟研究进展

离子液体是由有机阳离子和无机/有机阴离子构成的盐类,一般在室温或接近于室温下呈液态,因此常被称为室温离子液体(RTIL).依据不同的划分标准,离子液体有多种分类方式:根据年代的不同可将离子液体分为第一代、第二代及第三代离子液体,例如:烷基咪唑和烷基吡啶的金属卤化物盐等[1];根据阳离子的不同可将离子液体分为季鏻     

Reaction mechanism of soluble epoxide hydrolase: insights from molecular dynamics simulations

Molecular dynamics simulations have been performed to gain insights into the catalytic mechanism of the hydrolysis of epoxides to vicinal diols by soluble epoxide hydrolase (sEH). The binding of a substrate, 1S,2S-trans-methylstyrene oxide, was studied in two conformations in the active site of the enzyme. It was found that only one is likely to be found in the active enzyme. In the preferred conformation the phenyl group of the substrate is pi-sandwiched between two aromatic residues, Tyr381 and His523, whereas the other conformation is pi-stacked with only one aromatic residue, Trp334. Two simulations were carried out to 1 ns for each conformation to evaluate the protonation state of active site residue His523. It was found that a protonated histidine is essential for keeping the active site from being disrupted. Long time scale, 4 ns, molecular dynamics simulation was done for the structure with the most likely combination of binding conformation and protonation state of His523. Near Attack Conformers (NACs) are present 5.3% of the time and nucleophilic attack on either epoxide carbon atom, approximately 75% on C(1) and approximately 25% on C(2), is found. A maximum of one hydrogen bond between the epoxide oxygen and either of the active site tyrosines, Tyr465 and Tyr381, is present, in agreement with experimental mutagenesis results that reveal a slight loss in activity if one tyrosine is mutated and essential loss of all activity upon double mutation of the two tyrosines in question. It was found that a hydrogen bond from Tyr465 to the substrate oxygen is essential for controlling the regioselectivity of the reaction. Furthermore, a relationship between the presence of this hydrogen bond and the separation of reactants was found. Two groups of amino acid segments were identified each as moving collectively. Furthermore, an overall anti-correlation was found between the movements of these two individually collectively moving groups, made up by parts of the cap-region, including the two tyrosines, and the site of the catalytic triad, respectively. This overall anti-correlated collective domain motion is, perhaps, involved in the conversion of E.NAC to E.TS.     

Preparation and properties of immobilized diphtheria toxin

Commercially available diphtheria toxin was immobilized on nylon stocking material by a covalent activation of the polymeric material. Toxin was bound both directly to nylon as well as to nylon-polyethyleneimine copolymer. The immobilized toxin retained some of its catalytic activity as evidenced by ADP-ribosylation of elongation factor II. Kinetics of this reaction are reported. After repeated use for several times the immobilized toxin retains 75% of its activity.     

An analysis of ATP binding with kinase catalytic subunit by molecular dynamics simulation of the CDK2 active kinase crystal lattice

Molecular dynamics simulation was used to analyze changes in the functionally significant structural elements of the crystal lattices of pT160-CDK2/cyclin and A/ATP-Mg²⁺/substrate complexes of the native (CDK2-G16) and mutant (CDK2-S16) active kinases at physiological temperatures (300 K). The structural rearrangement of ATP caused by changes in the kinase catalytic domain was studied. ATP was fixed by the ionic and H-bond interactions of several residues, including Lys33, Asp145, and side-chain amides of the G loop between β1 and β2. The binding of the kinases to complexes with cyclin and the phosphorylation of T160 in the active complex of the CDK2 kinase result in the ATP orientation more convenient for the transfer of the phosphate group to the substrate. An analysis of interatomic distances in the ATP active site region and Asp145, Asn132, Lys33 catalytic sites participating in the orientation of ATP phosphates revealed that the Asp 145 amino acid residue was situated noticeably closer to the ATP molecule in the native complex than in its mutant counterpart. The same is true of the arrangement of the Lys33 residue with respect to ATP.     

R(-)四氢噻唑-2-硫酮-4-羧酸对D,L-氨基酸酯拆分的研究

以新手性拆分试剂R(-)四氢噻唑-2-硫酮-4-羧酸[简称R(-)TTCA]对D,L-氨基酸酯进行手性拆分,分别得到(R)TTCA氨基酸酯盐1a_1f([α]_D²⁰＝-30.40°～-42.70°)及光学活性氨基酸酯2a-2f,其光学纯度为35.4%～75.8%.由1a_1f在碱存在下分解出2a-2f的对映体3a-3f,光学纯度为39.50%～69.10%.用半经验的量子化学PM3方法研究了氨基的碱性、中间产物铵盐生成热和稳定性.     

Role of Tyr-435 of <Emphasis Type="Italic">Vibrio harveyi</Emphasis> Chitinase A in Chitin Utilization

Vibrio harveyi chitinase A or VhChiA (EC.3.2.1.14) is a member of GH-18 chitinases that catalyzes chitin degradation from marine biomaterials. Our earlier structural data of VhChiA suggested that Tyr-435 marks the ending of subsite +2 and may influence binding of the interacting substrate at the aglycone binding sites. This study reports the effects of Tyr-435 using site-directed mutagenesis technique. Mutation of Tyr-435 to Ala (mutant Y435A) enhanced both binding and catalytic efficiency of VhChiA, whereas substitution of Tyr-435 to Trp (mutant Y435W) lessened the ability of the enzyme to bind and hydrolyze chitin substrates. The increased activity of Y435A can be explained by partial removal of a steric clash around subsite (+2), thereby allowing a chitin chain to move beyond or to access the enzyme’s active site from the aglycone side more straightforwardly.     

Why substituting the asparagine at position 35 in Bacillus circulans xylanase with an aspartic acid remarkably improves the enzymatic catalytic activity? A quantum chemistry-based calculation study

Xylanases from Bacillus circulans (BCX) are known as configuration-retaining glycoside hydrolases, which hydrolyze xylans with two glutamic acid residues (Glu78 and Glu172) serving as catalytic active residues according to a double displacement mechanism. Existing experimental researches show that mutating the asparagines (Asn) to aspartic acid (Asp) at position 35 next to Glu172 can obviously improve the catalytic activity of BCX. To better understand the inherent mechanism for the experimental finding, we performed quantum chemistry calculations on two model systems to mimic the catalyses of wild-type and mutant BCXs. Geometrical structures and relative energies of intermediates and transition states involved in the hydrolysis reactions are given in detail. It is found that in the wild-type model system Asn35 interacts with Glu172 via a loose hydrogen bond, while in the mutant model system Asp35 forms a very tight hydrogen bond with Glu172. The glycosidic bond cleavage is proposed to be the rate-determining step for the hydrolysis reaction, whose barrier varies from 98 to 65 kJ mol⁻¹ when Asn35 is replaced by Asp35, showing the presence of Asp35 remarkably reduces the energy demand for the hydrolysis reaction. The present result provides a theoretical elucidation for why a single amino acid substitution can importantly influences catalytic activity of BCX.