Structural Basis of Epitope Recognition by Heavy-Chain Camelid Antibodies

Truncated versions of heavy-chain antibodies (HCAbs) from camelids, also termed nanobodies, comprise only one-tenth the mass of conventional antibodies, yet retain similar, high binding affinities for the antigens. Here we analyze a large data set of nanobody–antigen crystal structures and investigate how nanobody–antigen recognition compares to the one by conventional antibodies. We find that nanobody paratopes are enriched in aromatic residues just like conventional antibodies, but additionally, they also bear a more hydrophobic character. Most striking differences were observed in the characteristics of the antigen's epitope. Unlike conventional antibodies, nanobodies bind to more rigid, concave, conserved and structured epitopes enriched with aromatic residues. Nanobodies establish fewer interactions with the antigens compared to conventional antibodies, and we speculate that high binding affinities are achieved due to less unfavorable conformational and more favorable solvation entropy contributions. We observed that interactions with antigen are mediated not only by three CDR loops but also by numerous residues from the nanobody framework. These residues are not distributed uniformly; rather, they are concentrated into four structurally distinct regions and mediate mostly charged interactions. Our findings suggest that in some respects nanobody–antigen interactions are more similar to the general protein–protein interactions rather than antibody–antigen interactions.     

Mechanistic analysis of allosteric and non-allosteric effects arising from nanobody binding to two epitopes of the dihydrofolate reductase of Escherichia coli

Although allosteric effector antibodies are used widely as modulators of receptors and enzymes, experimental analysis of their mechanism remains highly challenging. Here, we investigate the molecular mechanisms of allosteric and non-allosteric effector antibodies in an experimentally tractable system, consisting of single-domain antibodies (nanobodies) that target the model enzyme dihydrofolate reductase (DHFR) from Escherichia coli. A panel of thirty-five nanobodies was isolated using several strategies to increase nanobody diversity. The nanobodies exhibit a variety of effector properties, including partial inhibition, strong inhibition and stimulation of DHFR activity. Despite these diverse effector properties, chemical shift perturbation NMR epitope mapping identified only two epitope regions: epitope α is a new allosteric site that is over 10 Å from the active site, while epitope β is located in the region of the Met20 loop. The structural basis for DHFR allosteric inhibition or activation upon nanobody binding to the α epitope was examined by solving the crystal structures of DHFR in complex with Nb113 (an allosteric inhibitor) and Nb179 (an allosteric activator). The structures suggest roles for conformational constraint and altered protein dynamics, but not epitope distortion, in the observed allosteric effects. The crystal structure of a β epitope region binder (ca1698) in complex with DHFR is also reported. Although CDR3 of ca1698 occupies the substrate binding site, ca1698 displays linear mixed inhibition kinetics instead of simple competitive inhibition kinetics. Two mechanisms are proposed to account for this apparent anomaly. Evidence for structural convergence of ca1698 and Nb216 during affinity maturation is also presented.     

Plasminogen activator in prostatic tumors of Nb rats

Using a fluorometric assay, nonspecific proteolytic activity and plasminogen activator were measured in transplantable tumors of the dorsal prostate of Nb rats. Nonspecific proteolytic activity in prostatic tumors did not differ significantly from that measured in normal dorsal prostate, whereas plasminogen activator activity, undetectable in the latter tissue, was readily measurable in the tumors. Furthermore, plasminogen activator in prostatic tumors characterized by hormone-insensitive growth was 8-fold higher than in tumors characterized by androgen-stimulated growth. In both types of tumors, the plasminogen activator activity per mg protein was highest in the lysosomal fractions. The result indicate that plasminogen activator may be a useful marker for discriminating between androgen-stimulated and autonomous prostatic tumors.     

纳米抗体技术及其在疾病诊断和治疗中的应用

单克隆抗体具有特异性结合抗原的能力,已被广泛应用于疾病诊断及治疗领域.但因单克隆抗体的组织渗透能力较差、体内的保留时间较长以及制备过程繁琐,从而限制了其在临床中的应用.自1993年首次报道在骆驼体内天然存在的单链抗体(HCAb)以来,由于其可变区间VHH(纳米抗体)具有体积小、溶解度高、特异性强以及可在细菌中大量表达等优点,较之传统单克隆抗体,VHH在疾病的诊断治疗及药物开发等医学领域具有更广阔的应用前景.本文综述了:纳米抗体的骨架区及互补决定区与传统抗体重链相应区间的结构比较;纳米抗体库的构建以及运用噬菌体展示技术对VHH库的筛选;纳米抗体技术在疾病诊断中的应用及其用于分子显像的优势,以及纳米抗体作为抗肿瘤免疫偶联物的靶向组分在癌症治疗领域中的最新进展.     

Molecular characterisation and regulation of a Nicotiana tabacum S-domain receptor-like kinase gene induced during an early rapid response to lipopolysaccharides

The isolation, characterization and regulation of the first lipopolysaccharide (LPS)-responsive S-domain receptor-like kinase (RLK) in Nicotiana tabacum are reported. The gene, corresponding to a differentially expressed LPS-responsive EST, was fully characterised to investigate its involvement in LPS-induced responses. The full genomic sequence, designated Nt-Sd-RLK, encodes for a S-domain RLK protein containing conserved modules (B-lectin-, S- and PAN-domains) reported to function in mediating protein-protein and protein-carbohydrate interactions in its extracellular domain, as well as the molecular architecture to transduce signals intracellularly through a Ser/Thr kinase domain. Phylogenetic analysis clustered Nt-Sd-RLK with S-domain RLKs induced by bacteria, wounding and salicylic acid. Perception of LPS induced a rapid, bi-phasic response in Nt-Sd-RLK expression with a 17-fold up-regulation at 3 and 9h. A defence-related W-box cis element was found in the promoter region of Nt-Sd-RLK and the transient induction of Nt-Sd-RLK in cultured cells by LPS exhibited a pattern typical of early response defence genes. Nt-Sd-RLK was also responsive to salicylic acid induction and was expressed in differentiated leaf tissue, where LPS elicited local as well as systemic up-regulation. The results contribute new knowledge about the potential role that S-domain RLKs may play within interactive signal transduction pathways associated with immunity and defence.     

Constraining enzyme conformational change by an antibody leads to hyperbolic inhibition

Although it has been known for many years that antibodies display properties characteristic of allosteric effectors, the molecular mechanisms responsible for these effects remain poorly understood. Here, we describe a single-domain antibody fragment (nanobody) that modulates protein function by constraining conformational change in the enzyme dihydrofolate reductase (DHFR). Nanobody 216 (Nb216) behaves as a potent allosteric inhibitor of DHFR, giving rise to mixed hyperbolic inhibition kinetics. The crystal structure of Nb216 in complex with DHFR reveals that the nanobody binds adjacent to the active site. Half of the epitope consists of residues from the flexible Met20 loop. This loop, which ordinarily oscillates between occluded and closed conformations during catalysis, assumes the occluded conformation in the Nb216-bound state. Using stopped flow, we show that Nb216 inhibits DHFR by stabilising the occluded Met20 loop conformation. Surprisingly, kinetic data indicate that the Met20 loop retains sufficient conformational flexibility in the Nb216-bound state to allow slow substrate turnover to occur.     

Protective effect of prolactin and placental lactogen on NO-induced Nb2 lymphoma cell apoptosis

Nitric oxide (NO) is an important modulator involved in immune regulation. Here, we describe conditions under which NO-donors induce apoptosis on Nb2 lymphoma cells, as evidenced by decreased cell viability and increased hypodiploid DNA content determined by flow cytometry. In addition, DNA fragmentation typical of apoptosis was shown by agarose gel electrophoresis. This apoptosis was accompanied by a significant increase of caspase-3-like enzymatic activity. Both ovine prolactin (oPRL) and ovine placental lactogen (oPL) exerted a protective effect on the NO-donor-induced apoptosis. Furthermore, dexamethasone (Dex)-induced cell death was also associated with caspase-3-like activity and oPL had the same potency as oPRL in its protective effect on Dex-induced apoptosis of Nb2 cells.     

Molecular cloning,characterization, and expression studies of water buffalo (<Emphasis Type="Italic">Bubalus bubalis</Emphasis>) somatotropin

Cloning, high-level expression, and characterization of the somatotropin (ST) gene of an indigenous Nili-Ravi breed of water buffalo Bubalus bubalis (BbST) are described. Coding, non-coding, and promoter regions of BbST were amplified and sequenced. Sequence analysis revealed several silent and two interesting point mutations on comparison with STs of other vertebrate species. One interesting variation in the BbST sequence was the replacement of a conserved glutamine residue by arginine. A plasmid was also constructed for the production of BbST in Escherichia coli BL21 (RIPL) CodonPlus, under the control of IPTG-inducible T7-lac promoter. High-level expression could be obtained by synthesizing a codon-optimized ST gene and expressing it in the form of inclusion bodies. The inclusion bodies represented over 20% of the E. coli cellular proteins. The biologically active conformation of purified BbST was confirmed by its efficient growth promoting activity in Nb2 cell proliferation assay. The expression system and purification strategy employed promise to be a useful approach to produce BbST for further use in structure—function studies and livestock industry. Published in Russian in Biokhimiya, 2007, Vol. 72, No. 2, pp. 194–202.     

Identification of Phase Control of Carbon‐Confined Nb2O5 Nanoparticles toward High‐Performance Lithium Storage

Niobium pentoxides (Nb₂O₅) have attracted extensive interest for ultrafast lithium‐ion batteries due to their impressive rate/capacity performance and high safety as intercalation anodes. However, the intrinsic insulating properties and unrevealed mechanisms of complex phases limit their further applications. Here, a facile and efficient method is developed to construct three typical carbon‐confined Nb₂O₅ (TT‐Nb₂O₅@C, T‐Nb₂O₅@C, and H‐Nb₂O₅@C) nanoparticles via a mismatched coordination reaction during the solvothermal process and subsequent controlled heat treatment, and different phase effects are investigated on their lithium storage properties on the basis of both experimental and computational approaches. The thin carbon coating and nanoscale size can endow Nb₂O₅ with a high surface area, high conductivity, and short diffusion length. As a proof‐of‐concept application, when employed as LIB anode materials, the resulting T‐Nb₂O₅@C nanoparticles display higher rate capability and better cycling stability as compared with TT‐Nb₂O₅@C and H‐Nb₂O₅@C nanoparticles. Furthermore, a synergistic effect is investigated and demonstrated between fast diffusion pathways and stable hosts in T‐Nb₂O₅ for ultrafast and stable lithium storage, based on crystal structure analysis, in situ X‐ray diffraction analysis, and density functional theoretical calculations. Therefore, the proposed synthetic strategy and obtained deep insights will stimulate the development of Nb₂O₅ for ultrafast and long‐life LIBs.