抗脂多糖纳米抗体的筛选及其五聚体的制备

目的：筛选抗脂多糖（LPS）纳米单域抗体,并制备抗LPS纳米抗体五聚体。方法：以LPS为抗原,从驼源天然单域重链抗体库中筛选抗LPS纳米抗体,利用分子克隆技术将抗LPS单域抗体基因组装入志贺杆菌样毒素B亚基蛋白结构域（VTB）的五聚体特异性表达载体中进行可溶性表达,并用ELISA法鉴定所获抗体的抗原结合活性和特异性。结果：获得抗LPS纳米单域抗体及LPS纳米抗体五聚体;经鉴定,LPS纳米抗体五聚体的抗原结合活性优于抗LPS单域抗体。结论：利用驼源天然单域重链抗体库制备了抗LPS纳米单域抗体及抗LPS纳米抗体五聚体,为脓毒血症的分子诊断、预后判断及寻找生物治疗新靶点奠定了基础。     

研究报告：金抗体替代ELISA中的天然抗体用于溶菌酶检测

目的酶联免疫吸附测定(ELISA)被广泛用于抗体或抗原的检测,并被视为临床实践中的金标准,可提供相对可靠、灵敏和特异的检测结果。ELISA的本质是抗原与相应抗体之间的特异性相互作用。然而,天然抗体固有的不稳定性是ELISA的一个难以克服的弱点,并可能导致检测结果的重现性差甚至错误的诊断结果。本课题组先前应用构象工程方法开发了一种基于金纳米粒子的人工抗体(简称金抗体)。金抗体可以像天然抗体一样特异性地与抗原相互作用,并且具备远优于天然抗体的稳定性。出色的稳定性使金抗体可能成为天然抗体更好的替代物,用于ELISA中。方法经过必要的优化并与辣根过氧化物酶(HRP)耦联后,制得酶标金抗体10HRP-(Au-400P1),然后用酶标金抗体代替天然酶标抗体用于ELISA检测中。结果通过一系列的实验证明,抗溶菌酶金抗体可用于ELISA特异性检测1～16 mg/L范围内的鸡蛋清溶菌酶(HEWL)样品。结论金抗体可以替代天然抗体用于ELISA检测,并具有优于传统ELISA法的检测准确性和一致性。     

抗体和寡核苷酸双标记纳米金生物探针的制备及性能分析

基于纳米金粒子与抗体静电吸附作用,与硫醇修饰的寡核苷酸共价结合,建立一种新的双标记纳米金生物探针的制备方法.通过透射电镜（TEM）、紫外光谱、斑点免疫金渗滤法、免疫金银染色光镜观察法、荧光标记法等检测探针表征,及表面抗体活性情况和寡核苷酸的覆盖率,同时采用变性聚丙烯酰胺凝胶电泳（PAGE）检测寡核苷酸的存在.结果表明,纳米金粒子同时连接抗体和寡核苷酸后生物性能良好,且每个纳米金粒子（10±3）nm表面可覆盖寡核苷酸(92±20)条,双标记纳米金生物探针的制备具有简捷、稳定的特点.可作为一种新型探针应用于超微量蛋白质检测.     

基于GFP的FRET应用

绿色荧光蛋白（GFP）是一种活性荧光标记,已被用来研究基因表达、分子定位,蛋白质折叠和转运;荧光共振能量转移（FRET）是一种无损伤的光学检测方法,能检测到小于纳米的距离变化。将GFP的活性定位标记功能与FRET的高分辨率相结合。为活体研究生物分子的功能和命运开创了新的篇章。作者在介绍GFP和FRET原理的基础上,综述了基于GFP的FRET在蛋白酶活性,蛋白质间相互作用 构象改变研究中的应用。     

人源中和性抗甲型肝炎病毒抗体Fab段基因的序列分析及可溶性表达

在用噬菌体表面呈现系统获得人源抗甲型肝炎（甲肝）病毒中和发生基因工程Fab抗体的基础上,对所获得的4株中和性Fab抗体轻重链可变区进行了序列分析、可溶性表达及生物学特性鉴定。4株Fab抗体重链可变区拥有99％同源的核苷酸序列和相同的CDR区氨基酸序列,属于VHⅢ基因家族,而轻链可变区核苷酸序列同源性为95％和相似的CDR区氨基酸序列,属于VL5基因家族。这些重组抗体都能与人甲肝恢复期血清及具有中和活性的鼠抗甲肝克隆抗体产生竞争抑制反应,表明其针对甲肝癌病毒结构蛋白上的主要抗的决定簇。     

重组裂殖子表面蛋白质1特异性抗体有效抑制恶性疟原虫体外生长

42kD恶性疟原虫裂殖子表面蛋白质 1C末端片段 (MSP1 42 )是当今重要的疟疾疫苗候选抗原。为获得大量构象正确的MSP1 42重组蛋白进行疫苗有效性试验 ,在毕氏酵母系统中分泌表达了MSP1 42重组蛋白。通过与一组特异性识别构象表位的单抗反应 ,该重组蛋白在重要构象表位上与天然蛋白质一致。由该蛋白质诱生的抗体能有效地抑制恶性疟原虫的体外生长 ,这些结果为进一步开展MSP1 42重组蛋白疫苗有效性试验提供了基础     

萤火虫荧光素酶单克隆抗体的制备与抗原决定簇的研究

以大肠杆菌表达的萤火虫荧光素酶 (fireflyluciferase)为抗原 ,免疫小鼠并进一步筛选与克隆 ,共得到 6株单克隆抗体 .制备腹水并纯化获得抗体后 ,对这 6株抗体与天然态和热变性态蛋白质以及蛋白酶解片段的结合性质进行了鉴定 .认为这 6株抗体的抗原决定簇都是顺序决定簇 .发现其中有 2株单抗与热变性态蛋白质及酶解片段的结合能力较强 ,而不与天然态蛋白质结合 ,其抗原决定簇可能是位于蛋白质内部的肽段 .另外 4株抗体既可与热变性态蛋白质以及酶解片段结合 ,也可与天然态蛋白质结合 ,其抗原决定簇可能位于蛋白质分子表面 .     

核磁共振技术在蛋白质领域的应用

简要叙述了核磁共振技术(NMR)在蛋白质领域的研究及应用。NMR法通过测定蛋白质在稀溶液状态下反应位点的特定参数来计算蛋白质的三级结构,并可深入了解一定时间范围内化学反应和蛋白质构象转变的动力学过程。通过NMR对抗原决定簇和抗体CDR作图,可以分析其一级结构和三维构象;对抗原抗体动力学的分析,对于设计基因疫苗、检测细胞表面抗原提呈以及分析抗原抗体复合物的构象变化也有着重要意义。     

鼠抗人纤维蛋白抗体单链Fv片段的人源化分子设计

产生免疫原性的残基主要是位于蛋白表面的暴露残基,为了消除鼠抗体对人的免疫原性,利用表面再塑的方法对本室克隆的鼠抗人纤维蛋白抗体单链Ｆｖ片段进行了人源化分子设计．首先确定了鼠及人Ｆｖ片段的表面残基,在此基础上分析了鼠与人抗体Ｆｖ片段表面残基的差异,将存在差异的鼠抗体的表面残基换成人的,从而实现鼠抗体的人源化．提出了残基最高频率人源化及最相似链人源化两种分子设计方案．人源化的鼠抗人纤维蛋白抗体单链Ｆｖ片段的结构经Ｐｒｏｆｉｌｅｓ－３Ｄ检测证明合理,替换的表面残基的溶剂可及性未变,而且未对ＣＤＲｓ的空间构象产生明显影响,应不会影响与纤维蛋白的亲和力,为鼠抗体人源化实验研究奠定了基础．     

以Ca-Ca距离为基础的构象空间的可视化研究

蛋白质结构构象呈现明显的规律,研究其在特定构象空间的分布对蛋白质结构预测和模拟具有重要意义。本文以449个非冗余的高分辨串蛋白质结构为材料,以Ga-Ga距离向量代表蛋白质片段。然后利用主成分分析方法,建立蛋白质片段构象空间的可视化构图,并且单个蛋白质分子可以映射到该空间形成一个顺序连接的路径。从而,可以很直观的分析各长度片段（4-9个残基的片段）的分布情况及其内在的连接关系。图形显示了明显的聚集性,以及各种类型片段与二级结构明显的对应关系。     

Multi‐constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility

The limited size of the germline antibody repertoire has to recognize a far larger number of potential antigens. The ability of a single antibody to bind multiple ligands due to conformational flexibility in the antigen‐binding site can significantly enlarge the repertoire. Among the six complementarity determining regions (CDRs) that generally comprise the binding site, the CDR H3 loop is particularly variable. Computational protein design studies showed that predicted low energy sequences compatible with a given backbone structure often have considerable similarity to the corresponding native sequences of naturally occurring proteins, indicating that native protein sequences are close to optimal for their structures. Here, we take a step forward to determine whether conformational flexibility, believed to play a key functional role in germline antibodies, is also central in shaping their native sequence. In particular, we use a multi‐constraint computational design strategy, along with the Rosetta scoring function, to propose that the native sequences of CDR H3 loops from germline antibodies are nearly optimal for conformational flexibility. Moreover, we find that antibody maturation may lead to sequences with a higher degree of optimization for a single conformation, while disfavoring sequences that are intrinsically flexible. In addition, this computational strategy allows us to predict mutations in the CDR H3 loop to stabilize the antigen‐bound conformation, a computational mimic of affinity maturation, that may increase antigen binding affinity by preorganizing the antigen binding loop. In vivo affinity maturation data are consistent with our predictions. The method described here can be useful to design antibodies with higher selectivity and affinity by reducing conformational diversity. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

CDR-H3 loop ensemble in solution – conformational selection upon antibody binding

ABSTRACT

We analyzed pairs of protein-binding, peptide-binding and hapten-binding antibodies crystallized as complex and in the absence of the antigen with and without conformational differences upon binding in the complementarity-determining region (CDR)-H3 loop. Here, we introduce a molecular dynamics-based approach to capture a diverse conformational ensemble of the CDR-H3 loop in solution. The results clearly indicate that the inherently flexible CDR-H3 loop indeed needs to be characterized as a conformational ensemble. The conformational changes of the CDR-H3 loop in all antibodies investigated follow the paradigm of conformation selection, because we observe the experimentally determined binding competent conformation without the presence of the antigen within the ensemble of pre-existing conformational states in solution before binding. We also demonstrate for several examples that the conformation observed in the antibody crystal structure without antigen present is actually selected to bind the carboxyterminal tail region of the antigen-binding fragment (Fab). Thus, special care must be taken when characterizing antibody CDR-H3 loops by Fab X-ray structures, and the possibility that pre-existing conformations are present should always be considered.     

Structural diversity in a human antibody germline library

To support antibody therapeutic development, the crystal structures of a set of 16 germline variants composed of 4 different kappa light chains paired with 4 different heavy chains have been determined. All four heavy chains of the antigen-binding fragments (Fabs) have the same complementarity-determining region (CDR) H3 that was reported in an earlier Fab structure. The structure analyses include comparisons of the overall structures, canonical structures of the CDRs and the VH:VL packing interactions. The CDR conformations for the most part are tightly clustered, especially for the ones with shorter lengths. The longer CDRs with tandem glycines or serines have more conformational diversity than the others. CDR H3, despite having the same amino acid sequence, exhibits the largest conformational diversity. About half of the structures have CDR H3 conformations similar to that of the parent; the others diverge significantly. One conclusion is that the CDR H3 conformations are influenced by both their amino acid sequence and their structural environment determined by the heavy and light chain pairing. The stem regions of 14 of the variant pairs are in the ‘kinked’ conformation, and only 2 are in the extended conformation. The packing of the VH and VL domains is consistent with our knowledge of antibody structure, and the tilt angles between these domains cover a range of 11 degrees. Two of 16 structures showed particularly large variations in the tilt angles when compared with the other pairings. The structures and their analyses provide a rich foundation for future antibody modeling and engineering efforts.     

Humanization of a murine monoclonal antibody by simultaneous optimization of framework and CDR residues.

Optimal protein function often depends on co-operative interactions between amino acid residues distant in the protein primary sequence yet spatially near one another following protein folding. For example, antibody affinity is influenced by interactions of framework residues with complementarity-determining region (CDR) residues. However, despite the abundance of antibody structural information and computational tools the humanization of rodent antibodies for clinical use often results in a significant loss of affinity. To date, antibody engineering efforts have focused either on optimizing CDR residues involved in antigen binding or on optimizing antibody framework residues that serve critical roles in preserving the conformation of CDRs. In the present study a new approach which permits the rapid identification of co-operatively interacting framework and CDR residues was used to simultaneously humanize and optimize a murine antibody directed against CD40. Specifically, a combinatorial library that examined eight potentially important framework positions concomitantly with focused CDR libraries consisting of variants containing random single amino acid mutations in the third CDR of the heavy and light chains was expressed. Multiple anti-CD40 Fab variants containing as few as one murine framework residue and displaying up to approximately 500-fold higher affinity than the initial chimeric Fab were identified. The higher affinity humanized variants demonstrated a co-operative interaction between light chain framework residue Y49 and heavy chain CDR3 residue R/K101 (coupling energy, DeltaGI=0.9 kcal/mol). Screening of combinatorial framework-CDR libraries permits identification of monoclonal antibodies (mAb) with structures optimized for function, including instances in which the antigen induces conformational changes in the mAb. Moreover, the enhanced humanized variants contain fewer murine framework residues and could not be identified by sequential in vitro humanization and affinity muturation strategies. This approach to identifying co-operatively interacting residues is not restricted to antibody-antigen interactions and consequently, may be used broadly to gain insight into protein structure-function relationships, including proteins that serve as catalysts.     

How the surface functionalized nanoparticles affect conformation and activity of proteins: Exploring through protein-nanoparticle interactions

To understand the effect of counter ions (Na⁺) on the secondary conformation and functionality of the lysozyme, we have studied the interaction of lysozyme with counterion associated iron oxide nanoparticles (IONPs). The investigation was carried out at pH 7.4 and 9.0, with three different types of NPs, namely, bare IONPs, low molecular weight chitosan modified IONPs (LMWC-IONPs) and the counterion (Na⁺) associated sodium tripolyphosphate IONPs (STP-LMWC-IONPs) and confirmed by using various spectroscopy techniques. The difference in UV–vis absorbance (ΔA) between native and STP-LMWC-IONPs interacted hen egg white lysozyme (HEWL) was greater than that between native and NPs interacted HEWL at pH 9.0 compared with pH 7.4. Furthermore, STP-LMWC-IONPs exhibited quenching effect on lysozyme fluorescence spectrum at pH 9.0 due to binding of Na⁺ counterions to the protein, confirming denaturation of the latter. After HEWL interaction with STP-LMWC-IONPs (pH 9.0), CD spectra revealed a conformational change in the secondary structure of HEWL. Also, counterion induced lysozyme inactivation, due to interaction with nanoparticles at pH 9.0, was confirmed by enzymatic activity assay involving lysis of Micrococcus lysodeikticus. In conclusion, pH 9.0 was observed to be a more favorable condition, compared to pH 7.4, for the strongest electrostatic interaction between lysozyme and NPs. We postulate that the counterions in nanoparticle surface-coating can ameliorate protein misfolding or unfolding and also prevent their aggregation and, therefore, can be considered as a powerful and potential therapeutic strategy to treat incurable neurodegenerative disorders.     

Structural effects of framework mutations on a humanized anti-lysozyme antibody.

A humanized version of the mouse anti-lysozyme Ab D1.3 was previously constructed as an Fv fragment and its structure was crystallographically determined in the free form and in complex with lysozyme. Here we report five new crystal structures of single-amino acid substitution mutants of the humanized Fv fragment, four of which were determined as Fv-lysozyme complexes. The crystals were isomorphous with the parent forms, and were refined to free R values of 28-31% at resolutions of 2.7-2.9 A. Residue 27 in other Abs has been implicated in stabilizing the conformation of the first complementarity-determining region (CDR) of the H chain, residues 31-35. We find that a Phe-to-Ser mutation at 27 alters the conformation of immediately adjacent residues, but this change is only weakly transmitted to Ag binding residues in the nearby CDR. Residue 71 of the H chain has been proposed to control the relative disposition of H chain CDRs 1 and 2, based on the bulk of its side chain. However, in structures we determined with Val, Ala, or Arg substituted in place of Lys at position 71, no significant change in the conformation of CDRs 1 and 2 was observed.     

Does conformational free energy distinguish loop conformations in proteins?

Limitations in protein homology modeling often arise from the inability to adequately model loops. In this paper we focus on the selection of loop conformations. We present a complete computational treatment that allows the screening of loop conformations to identify those that best fit a molecular model. The stability of a loop in a protein is evaluated via computations of conformational free energies in solution, i.e., the free energy difference between the reference structure and the modeled one. A thermodynamic cycle is used for calculation of the conformational free energy, in which the total free energy of the reference state (i.e., gas phase) is the CHARMm potential energy. The electrostatic contribution of the solvation free energy is obtained from solving the finite-difference Poisson-Boltzmann equation. The nonpolar contribution is based on a surface area-based expression. We applied this computational scheme to a simple but well-characterized system, the antibody hypervariable loop (complementarity-determining region, CDR). Instead of creating loop conformations, we generated a database of loops extracted from high-resolution crystal structures of proteins, which display geometrical similarities with antibody CDRs. We inserted loops from our database into a framework of an antibody; then we calculated the conformational free energies of each loop. Results show that we successfully identified loops with a "reference-like" CDR geometry, with the lowest conformational free energy in gas phase only. Surprisingly, the solvation energy term plays a confusing role, sometimes discriminating "reference-like" CDR geometry and many times allowing "non-reference-like" conformations to have the lowest conformational free energies (for short loops). Most "reference-like" loop conformations are separated from others by a gap in the gas phase conformational free energy scale. Naturally, loops from antibody molecules are found to be the best models for long CDRs (> or = 6 residues), mainly because of a better packing of backbone atoms into the framework of the antibody model.     

AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences

Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function—essential to exert control over all polypeptide degrees of freedom—remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high‐affinity antibodies; in five cases interface sequence identity is above 30%, and in four of those the backbone conformation at the core of the antibody binding surface is within 1 Å root‐mean square deviation from the natural antibodies. Designs recapitulate polar interaction networks observed in natural complexes, and amino acid sidechain rigidity at the designed binding surface, which is likely important for affinity and specificity, is high compared to previous design studies. In designed anti‐lysozyme antibodies, complementarity‐determining regions (CDRs) at the periphery of the interface, such as L1 and H2, show greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, potentially enhancing affinity and specificity. Proteins 2015; 83:1385–1406. © 2015 Wiley Periodicals, Inc.     

Exploring single-domain antibody thermostability by molecular dynamics simulation

Abstract

Single-domain antibodies also known as nanobodies are recombinant antigen-binding domains that correspond to the heavy-chain variable region of camelid antibodies. Previous experimental studies showed that the nanobodies have stable and active structures at high temperatures. In this study, the thermal stability and dynamics of nanobodies have been studied by employing molecular dynamics simulation at different temperatures. Variations in root mean square deviation, native contacts, and solvent-accessible surface area of the nanobodies during the simulation were calculated to analyze the effect of different temperatures on the overall conformation of the nanobody. Then, the thermostability mechanism of this protein was studied through calculation of dynamic cross-correlation matrix, principal component analyses, native contact analyses, and root mean square fluctuation. Our results manifest that the side chain conformation of some residues in the complementarity-determining region 3 (CDR3) and also the interaction between α-helix region of CDR3 and framework2 play a critical role to stabilize the protein at a high temperature.

Communicated by Ramaswamy H. Sarma     

Lysozyme Folded In Silico According to the Limited Conformational Sub-space

Abstract

The conformational sub-space oriented on early-stage protein folding is applied to lysozyme folding. The part of the Ramachandran map distinguished on the basis of a geometrical model of the polypeptide chain limited to the mutual orientation of the peptide bond planes is shown to deliver the initial structure of the polypeptide for the energy minimization procedure in the ab initio model of protein folding prediction. Two forms of energy minimization and molecular dynamics simulation procedures were applied to the assumed early-stage protein folding of lysozyme. One of them included the disulphide bond system and the other excluded it. The post-energy-minimization and post-dynamics structures were compared using RMS-D and non-bonding contact maps to estimate the degree of approach to the native, target structure of the protein molecule obtained using the limited conformational sub-space for the early stage of folding.