Structural Insights into the Design of Synthetic Nanobody Libraries

Single domain antibodies from camelids, or nanobodies, are a unique class of antibody fragments with several advantageous characteristics: small monomeric size, high stability and solubility and easy tailoring for multiple applications. Nanobodies are gaining increasing acceptance as diagnostic tools and promising therapeutic agents in cancer and other diseases. While most nanobodies are obtained from immunized animals of the camelid family, a few synthetic nanobody libraries constructed in recent years have shown the capability of generating high quality nanobodies in terms of affinity and stability. Since this synthetic approach has important advantages over the use of animals, the recent advances are indeed encouraging. Here we review over a dozen synthetic nanobody libraries reported so far and discuss the different approaches followed in their construction and validation, with an emphasis on framework and hypervariable loop design as critical issues defining their potential as high-class nanobody sources.     

抗黄曲霉毒素B1多价纳米抗体融合蛋白的构建及活性分析

纳米抗体来源于天然缺失轻链的重链抗体可变区,是已知最小抗原结合单元.该研究构建了抗黄曲霉毒素B1(AFB1)纳米抗体的单价及多价串联体,分别与绿色荧光蛋白(GFP)编码片段融合并克隆至原核表达载体pET30.以大肠杆菌BL21(DE3)作为表达宿主,通过异丙基-β-D硫代吡喃半乳糖苷诱导,亲和层析技术分别纯化单、双及三...     

Automated Protein Structure Elucidation From 2D NMR

A general method for automated de novo deduction of protein structure from 2D NMR has been developed. The algorithms which extract simple spin coupling topologies from MQF-COSY, construct more complicated spin coupling topologies based upon MQ spectrum including all possible pathways, and extract spin coupling topological fragments for amino acids of a protein, have been implemented in C~(++) language and run on a SUN 4/280 work station. Compared with the manual assignments for melittin, the total identity of the automated de novo method is 86.3%.     

Influence of NMR Data Completeness on Structure Determinations of Homodimeric Proteins

The structure determination of homodimeric proteins by NMR using conventional NOESY experiments is still challenging due to the degeneracy of the chemical shifts in the identical monomers, which causes ambiguity in the NOE assignments. Residues involved in the interface between two monomers provide essential intermolecular NOEs for the structure determinations of homodimeric proteins. Hence NMR data, such as NOE peak lists and chemical shift assignments of these interface residues, play a crucial role for the successful structure determination of homodimeric proteins. This paper extends our previous report (Lin, Y.‐J.; Kirchner, D. K.; Güntert, P. J. Magn. Reson.­ 2012 , 222, 96) and investigates the influence of incomplete NOESY peak lists combined with incomplete ¹H chemical shift assignments of the interface residues on the structure determination of homodimeric proteins using the program CYANA. Data incompleteness was simulated by random omission of both NOESY cross peaks and interface ¹H chemical shifts. Our results for three proteins with different percentages of interface residues reveal that the algorithm can tolerate about 40–50% NOESY peak omission with complete interface chemical shift assignments, which indicates that partial NOESY peak omission does not cause severe problems when the interface chemical shifts are completely assigned. Combining NOESY peak omission with incomplete interface chemical shift assignments, the tolerance for interface chemical shift omission decreases with the extent of omitted NOESY peaks. The tolerance for unassigned interface side chain, methyl and aromatic chemical shifts is affected more strongly by NOESY peak omission than that for the omission of general interface ¹H chemical shifts including the backbone. In general about 10–30% peaks omission is tolerated in conjunction with missing chemical shift assignments. If more NOESY peaks are omitted calculations gradually become unstable and tend not to tolerate any missing interface chemical shifts. A large amount of omitted NOESY peaks, for instance 30% omission in our calculations, could decrease the tolerance for missing aromatic or methyl interface ¹H chemical shifts to as few as 2–4 missing chemical shifts, suggesting that complete aromatic and methyl ¹H chemical shift assignments are important when the NOESY peak data is significantly incomplete. Finally, for homodimeric proteins with a low percentage of interface residues, our results reveal that the omission of NOESY peaks, even at an extent of only 10%, can result in no tolerance against the omission of interface ¹H chemical shifts, suggesting that the completeness of both interface ¹H chemical shift assignments and NOESY peaks are important for the successful structure determination of proteins with a small homodimer interface.     

High‐Resolution NMR Determination of the Dynamic Structure of Membrane Proteins

¹⁵N spin‐relaxation rates are demonstrated to provide critical information about the long‐range structure and internal motions of membrane proteins. Combined with an improved calculation method, the relaxation‐rate‐derived structure of the 283‐residue human voltage‐dependent anion channel revealed an anisotropically shaped barrel with a rigidly attached N‐terminal helix. Our study thus establishes an NMR spectroscopic approach to determine the structure and dynamics of mammalian membrane proteins at high accuracy and resolution.     

Hybrid Structure of the Type 1 Pilus of Uropathogenic Escherichia coli

Type 1 pili are filamentous protein assemblies on the surface of Gram‐negative bacteria that mediate adhesion to host cells during the infection process. The molecular structure of type 1 pili remains elusive on the atomic scale owing to their insolubility and noncrystallinity. Herein we describe an approach for hybrid‐structure determination that is based on data from solution‐state NMR spectroscopy on the soluble subunit and solid‐state NMR spectroscopy and STEM data on the assembled pilus. Our approach is based on iterative modeling driven by structural information extracted from different sources and provides a general tool to access pseudo atomic structures of protein assemblies with complex subunit folds. By using this methodology, we determined the local conformation of the FimA pilus subunit in the context of the assembled type 1 pilus, determined the exact helical pilus architecture, and elucidated the intermolecular interfaces contributing to pilus assembly and stability with atomic detail.     

新型簇合物离子K+(KNO3)n和NO-3(KNO3)m

轴向配体在决定血红素蛋白结构和性能方面的作用引起人们的兴趣[1] .细胞色素 c是一个重要的电子传递蛋白 ,在天然状态下轴向配体 His 1 8和 Met80与血红素的 Fe原子配位 . UV光谱和 NMR谱显示氧化态细胞色素 c配位的 Met80在 p H大于 9或强外源配体存在时较易被取代[2 ] .人们对外源配体配位引发细胞色素 c的构象的研究得到一些重要的结构特征 [3,4 ] .但对整个蛋白溶液结构完整精确的描述和血红素电子结构的研究还很少 .此外 ,细胞色素 c在重折叠过程中形成组氨酸配位的中间体 ,而咪唑能捕获和阻断中间体的形成 .为此 ,本文对咪唑 -…     

Structure elucidation of casbane diterpenes from Croton argyrophyllus

Two novel casbane diterpenes 1-hydroxy-(2E,6Z,12E)-casba-2,6,12-triene-4,5-dione (1) and 6E,12E-casba-1,3,6,12-tetraen-1,4-epoxy-5-one (2) were isolated from the ethanol extract of the stems of Croton argyrophyllus. Structural characterization including the relative stereochemistry of all compounds was established on the basis of spectroscopic methods, mainly 1D and 2D NMR, and HRESIMS.     

Structure Analysis of Streptococcal Protein G Fc Binding Domain

The gene fragment (191 bp) encoding protein G IgG Fc binding domain was isolated by PCR from group G streptococcus (CMCC32138), and a clone containing this gene fragment was found to give fine reactivity to human IgG when expressed in Escherichia coli. The complete nucleotide sequence of the gene fragment was determined. One base pair differs from previously reported protein Gnucleotide sequences, and resultsin an amino acid change (Ala-Thr), but this variation makes no difference in binding to the IgG Fc part by ELISA.The secondary structure of the protein G IgG Fc binding domain has been estimated by circular dichroism and assigned by computer algorithm.It shows a typical α-helix region in this domain.By breaking this α-helix region with recombinant DNA techniques, a 44 peptide, which contained the N-terminal 27 amino acid residues of this domain, was expressed in E. coli and showed no reactivity to IgG.The hydropathicity of this domain was also analyzed and compared with that of protein A relevant     

Structure of Monomeric Transthyretin Carrying the Clinically Important T119M Mutation

Mutations in the protein transthyretin can cause as well as protect individuals from transthyretin amyloidosis, an incurable fatal inherited disease. Little is known, however, about the structural basis of pathogenic and clinically protective transthyretin mutants. Here we determined the solution structure of a transthyretin monomer that carries the clinically important T119M mutation. The structure displays a non‐native arrangement that is distinct from all known structures of transthyretin and highlights the importance of high‐resolution studies in solution for understanding molecular processes that lead to amyloid diseases.     

Structure of Nb/Ta layered ternary tellurides containing first row transition metal atoms

A summary of research on the structure of Nb/Ta layered tellurides in the past period is reported. 14 compounds, which have been structurally characterized by X-ray diffraction work, are presented according to their structural features. The first two compounds, Nb2CrTe4 and Nb2Cu1.48Te4, are characterized in that the ternary atoms are inserted in the different layers from the Nb atoms. While in the other compounds, both kinds of metal atoms are inserted in the same layer. The six compounds with formula M2M'2Te4(M = Nb/Ta; M' = Ni, Co, Fe) are characterized in that their structure can be described as construction by using cluster units "M2M'2Te10" as building blocks. in the two metal-rich compounds, TaCo2Te2 and TaNi2Te2, Ta atom has a distorted mono-capped pentagonal prism configuration. The structure of TaFeTe3, TaNTe3 and NbNi2.34Te3 can be described as building by the arrangement of double octahedral chains (DOC), in this con-nection, a selenide Ta2Ni2Se5 is also included by using the second type of     

ACD/Structure Elucidator: 20 Years in the History of Development

The first methods associated with the Computer-Assisted Structure Elucidation (CASE) of small molecules were published over fifty years ago when spectroscopy and computer science were both in their infancy. The incredible leaps in both areas of technology could not have been envisaged at that time, but both have enabled CASE expert systems to achieve performance levels that in their present state can outperform many scientists in terms of speed to solution. The computer-assisted analysis of enormous matrices of data exemplified 1D and 2D high-resolution NMR spectroscopy datasets can easily solve what just a few years ago would have been deemed to be complex structures. While not a panacea, the application of such tools can provide support to even the most skilled spectroscopist. By this point the structures of a great number of molecular skeletons, including hundreds of complex natural products, have been elucidated using such programs. At this juncture, the expert system ACD/Structure Elucidator is likely the most advanced CASE system available and, being a commercial software product, is installed and used in many organizations. This article will provide an overview of the research and development required to pursue the lofty goals set almost two decades ago to facilitate highly automated approaches to solving complex structures from analytical spectroscopy data, using NMR as the primary data-type.     

噻唑硫磷的结构研究

噻唑硫磷(fosthiazate)是一种新型、高效的有机磷农药。它是由2-氧化噻唑烷与S-仲丁基-O-乙基硫代磷酰氯通过取代反应制得,其化学名为O-乙基-S-仲丁基-2-氧代-1,3-噻唑烷-3-基硫代膦酸酯,结构式如下：     

Structure elucidation and NMR assignments of two unusual monoterpene indole alkaloids from Psychotria stachyoides

Two unusual monoterpene indole alkaloids, stachyoside ( 1 ) and nor‐methyl‐23‐oxo‐correantoside ( 2 ), have been isolated from the aerial parts of Psychotria stachyoides. The structural elucidation of both compounds was performed by the aid of HRESIMS, FT‐IR, and 1D‐ and 2D‐NMR techniques including COSY, HSQC, HMBC, and NOESY. Copyright © 2010 John Wiley & Sons, Ltd.     

Selective NMR Pulse Sequences for the Study of Solid Hydrogen‐Containing Fluoropolymers

Summary: Fluorine‐19 NMR spectra of solids have some special features, which are discussed in this article. In particular, they generally contain two abundant spin baths (protons and fluorine nuclei). This situation throws up some special operational requirements, as does the study of heterogeneous samples. The relaxation characteristics of heterogeneous systems, which are briefly described herein, frequently permit the use of specific pulse sequences to obtain subspectra for individual components. Various possible selective sequences for use in fluorinated heterogeneous organic solids are listed and their actions rationalized on the basis of molecular mobility. Semicrystalline hydrogen‐containing fluoropolymers form especially suitable systems for such operations, and in order to understand their domain structures it is essential to obtain subspectra of the amorphous and crystalline domains. Examples are given of the use of selective pulse sequences for studying fluoropolymers, especially for poly(vinylidene fluoride) (PVDF) and the copolymer P(VDF₇₅/TrFE₂₅) (TrFE = trifluoroethylene).

DIVAM/CP spectra of the vinylidene fluoride/trifluorethylene copolymer as a function of the minipulse angle used. Top: Unfiltered spectrum. Middle: the amorphous domains. Bottom: the crystalline domains.     

The Role of Conformations in the Interplay of Structure and Dynamics in Macromolecular and Supramolecular Systems

Summary: Following Paul J. Flory, the role of local chain conformation in determining the structure and dynamics of macromolecules is elucidated, employing advanced solid state NMR spectroscopy supported by X-ray scattering and dielectric spectroscopy. Topics covered include the local conformation in amorphous polymers, conformational memory, chain organization and dynamics in semicrystalline polymers, polypeptides, and rod-coil copolymers.     

Crystal‐Structure Determination of Powdered Paramagnetic Lanthanide Complexes by Proton NMR Spectroscopy

Shifts for crystals : Solid‐state NMR spectroscopy can be used for structure determination of microcrystalline paramagnetic solids at natural isotopic abundance. The protocol makes use of paramagnetic effects, measured on suitably recorded ¹H NMR spectra, to define the conformation of a molecule in the lattice and the intermolecular packing in the solid phase. The method is illustrated with a family of lanthanide compounds (see picture).