结构基因组学研究与核磁共振

各种生物的基因组DNA测序计划的完成,将结构生物学带入了结构基因组学时代.结构基因组学是对所有基因组产物结构的系统性测定,它运用高通量的选择、表达、纯化以及结构测定和计算分析手段,为基因组的每个蛋白质产物提供实验测定的结构或较好的理论模型,这将加速生命科学各个领域的研究.生物信息学、基因工程、结构测定技术等的发展为结构基因组学研究提供了保证.近年来核磁共振在技术方法上的进展,使其成为结构基因组学高通量结构分析中的一个关键方法.     

BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions

We describe the role of the BioMagResBank (BMRB) within the Worldwide Protein Data Bank (wwPDB) and recent policies affecting the deposition of biomolecular NMR data. All PDB depositions of structures based on NMR data must now be accompanied by experimental restraints. A scheme has been devised that allows depositors to specify a representative structure and to define residues within that structure found experimentally to be largely unstructured. The BMRB now accepts coordinate sets representing three-dimensional structural models based on experimental NMR data of molecules of biological interest that fall outside the guidelines of the Protein Data Bank (i.e., the molecule is a peptide with 23 or fewer residues, a polynucleotide with 3 or fewer residues, a polysaccharide with 3 or fewer sugar residues, or a natural product), provided that the coordinates are accompanied by representation of the covalent structure of the molecule (atom connectivity), assigned NMR chemical shifts, and the structural restraints used in generating model. The BMRB now contains an archive of NMR data for metabolites and other small molecules found in biological systems.     

The crystal structure of hypothetical protein MTH1491 from Methanobacterium thermoautotrophicum

As part of our structural proteomics initiative, we have determined the crystal structure of MTH1491, a previously uncharacterized hypothetical protein from Methanobacterium thermoautotrophicum. MTH1491 is one of numerous structural genomics targets selected in a genome-wide survey of uncharacterized proteins. It belongs to a family of proteins whose biological function is not known. The crystal structure of MTH1491, the first structure for this family of proteins, consists of an overall five-stranded parallel beta-sheet with strand order 51234 and flanking helices. The oligomeric form of this molecule is a trimer as seen from both crystal contacts and gel filtration studies. Analysis revealed that the structure of MTH1491 is similar to that of dehydrogenases, amidohydrolases, and oxidoreductases. Using a combination of sequence and structural analyses, we showed that MTH1491 does not belong to either the dehydrogenase or the amidohydrolase superfamilies of proteins.     

Caspase-12 cleavage and increased oxidative stress during motoneuron degeneration in transgenic mouse model of ALS

Glucose-dependent insulinotropic polypeptide is an incretin hormone that stimulates insulin secretion and reduces postprandial glycaemic excursions. The glucose-dependent action of GIP on pancreatic beta-cells has attracted attention towards its exploitation as a potential drug for type 2 diabetes. Use of NMR or X-ray crystallography is vital to determine the three-dimensional structure of the peptide. Therefore, to understand the basic structural requirements for the biological activity of GIP, the solution structure of the major biologically active fragment, GIP(1-30)amide, was investigated by proton NMR spectroscopy and molecular modelling. The structure is characterised by a full length alpha-helical conformation between residues F(6) and A(28). This structural information could play an important role in the design of therapeutic agents based upon GIP receptor agonists.     

Photoionization used as a tool for the study of biomembranes: fate of tetramethylbenzidine photocation in purple membrane

Photoionization of hydrophobic probes has been developed in micelles or synthetic vesicles. Studies of the yields, compartmentation, and lifetimes of the photo-produced charged species have gathered reliable information on the interfacial and structural properties of these assemblies. Such an approach has never been applied to biological membranes. The present system is tetramethylbenzidine as the probe in native or modified (deionized and/or bleached) purple membrane from halobacteria. The data on photocation formation yields (phi ion) and lifetimes (tau 1/2) allow two main conclusions to be made: (1) tetramethylbenzidine, as the cation, is buried in the membrane core, and (2) its incorporation does not alter the biological activity of the protein. In this biological membrane the photocation lifetime and yield present the same trend of variation with the surface potential but to less of an extent than in model membranes. Bleaching of purple membrane completely modifies the photoionization process and the photocation decay. In addition, these experiments reveal a tight correlation between membrane structure and probe photoionization. Further evidence for structural modification of purple membrane, either by deionization or by bleaching is pointed out.     

Understanding the molecular machinery of genetics through 3D structures

Detailed knowledge of the three-dimensional structures of biological molecules has had an enormous impact on all areas of biological science, including genetics, as structure can reveal the fine details of how molecules perform their biological functions. Here we consider how changes in protein sequence affect the corresponding 3D structure, and describe how structural information about proteins, DNA and chromatin has shed light on gene regulatory mechanisms and the storage and transmission of epigenetic information. Finally, we describe how structure determination is benefiting from the high-throughput technologies of the worldwide structural genomics projects.     

Effect of structural changes in thyroxine-binding globulin on its biological activity and immunochemical properties

Using spectroscopic, electrophoretic and microcalorimetric techniques, the changes in the spatial structure of human thyroxine-binding globulin (TBG) induced by exposure of protein solutions to high temperatures (45-90 degrees C) and low pH (2.5-6.0) were studied. Simultaneously the biological activity and immunoreactivity of TBG samples were measured. The structural changes were manifested at 52 degrees C or at pH 4.0 and were then aggravated with a rise in temperature or a decrease of pH. The circular dichroism spectra showed that the molecular ellipticity had a maximum decrease (by 10%) at 218-222 nm. In fluorescence spectra excitable at 280 nm the band half-width increased by 4-6 nm; their intensity decreased by 30-40%, whereas the position of the maxima did not change significantly. After addition of an equimolar amount of thyroxine to inactivated TBG the protein fluorescence was quenched by 25-40%. The electrophoregrams of treated preparations contained additional protein bands possessing no biological activity, whose mobility was less than that of native TBG. Microcalorimetric assays of native TBG revealed a thermoabsorption peak with a maximum at 62.5 degrees C and a half-width of 7.1 degrees C. The thermodynamic parameters of melting of TBG spatial structure were consistent with a model of a two-domain structure of the molecule. The biological activity and immunoreactivity of TBG showed a coordinated decrease with a rise in the degree of protein denaturation, However, the formation of TBG complex with antibodies did not screen the thyroxine-binding center of TBG and did not alter its affinity. Possible mechanisms of structural transition of TBG and its effect on the biological properties of TBG are discussed.     

Synthesis and evaluation of some steroidal oximes as cytotoxic agents: structure/activity studies (I)

The side chain of a compound plays an important role in its biological function. In our studies, we have found that hydroximinosteroid derivatives with different side chains and position of hydroximino on ring A and B displayed remarkable distinct cytotoxicities against a diversity of cancer cell types. Presence of an oxime group on ring B and a hydroxy on ring A or B resulted in a higher cytotoxicity than other structural motifs. In addition, a cholesterol-type side chain at position 17 was required for the biological activity. Our findings provide new evidence showing the relationship between the chemical structure and biological function. The information obtained from the studies may be useful for the design of novel chemotherapeutic drugs.     

Higher order structure of (1,3)-beta-D-glucans and its influence on their biological activities and complexation abilities

(1,3)-beta-D-Glucans form a group of biologically active biopolymers that exist in different structural organizations depending on the environmental conditions. The biological effect of (1,3)-beta-D-glucans is a core issue stimulating large research efforts of the molecular properties and their consequences for action as biological response modifiers. The fascination for these molecules increased further following the finding of their ability to form complexes of defined geometry with a number of structures, ranging from linear architectures as polymers or carbon nanotubes, to globular structures as gold particles or dye molecules. The fascinating information concerning the relationship between sample treatment history and molecular organization has not yet reached out to all the contributors within the field, resulting in unnecessary apparent inconsistencies in the literature. In addition to environmental conditions, the sample history is known to influence on the precise structural organization of these molecules. The present knowledge related to the structure of native as well as denatured, renatured and annealed (1,3)-beta-D-glucans is reviewed. The influence of their structural organization on the biological activity and complexation abilities is discussed, and some factors hindering progress in the understanding of their biological effects or complexation abilities are pointed out.     

Capturing time-resolved changes in molecular structure by negative staining

Imaging structural intermediates of biological processes is a key step in understanding biological function. Because intermediates are commonly short-lived, lasting only milliseconds, the main methods used to capture them have been conventional imaging of analog or inhibited states, having extended lifetimes, or rapid (millisecond timescale) freezing of intermediates with subsequent observation by cryo-EM. We have developed a simpler method that fixes structure on the millisecond timescale. The procedure consists of briefly (milliseconds) exposing the macromolecular structure of interest on an EM grid to conditions that initiate the structural change, then immediately fixing with uranyl acetate or tannic acid. Specimens are then observed by negative staining. The key finding that validates this approach is our demonstration that uranyl acetate, and in some cases tannic acid, fixes protein molecular structure on the millisecond timescale. This is demonstrated by our observation that exposure of actin and myosin filaments to these fixatives for as little as 10 ms is sufficient to fully preserve them against changes that normally induce rapid and major alteration in their molecular structure. Fixation appears to stabilize both ionic and hydrophobic bonds. This approach should be of general utility for studying transient molecular changes in many systems.     

Bioinformatic analysis of pathogenic missense mutations of activin receptor like kinase 1 ectodomain

Activin A receptor, type II-like kinase 1 (also called ALK1), is a serine-threonine kinase predominantly expressed on endothelial cells surface. Mutations in its ACVRL1 encoding gene (12q11-14) cause type 2 Hereditary Haemorrhagic Telangiectasia (HHT2), an autosomal dominant multisystem vascular dysplasia. The study of the structural effects of mutations is crucial to understand their pathogenic mechanism. However, while an X-ray structure of ALK1 intracellular domain has recently become available (PDB ID: 3MY0), structure determination of ALK1 ectodomain (ALK1(EC)) has been elusive so far. We here describe the building of a homology model for ALK1(EC), followed by an extensive bioinformatic analysis, based on a set of 38 methods, of the effect of missense mutations at the sequence and structural level. ALK1(EC) potential interaction mode with its ligand BMP9 was then predicted combining modelling and docking data. The calculated model of the ALK1(EC) allowed mapping and a preliminary characterization of HHT2 associated mutations. Major structural changes and loss of stability of the protein were predicted for several mutations, while others were found to interfere mainly with binding to BMP9 or other interactors, like Endoglin (CD105), whose encoding ENG gene (9q34) mutations are known to cause type 1 HHT. This study gives a preliminary insight into the potential structure of ALK1(EC) and into the structural effects of HHT2 associated mutations, which can be useful to predict the potential effect of each single mutation, to devise new biological experiments and to interpret the biological significance of new mutations, private mutations, or non-synonymous polymorphisms.     

Structure of HCV IRES domain II determined by NMR

Complex RNA structures regulate many biological processes, but are often too large for structure determination by NMR methods. The 5' untranslated region (5' UTR) of the hepatitis C viral (HCV) RNA genome contains an internal ribosome entry site (IRES) that binds to 40S ribosomal subunits with high affinity and specificity to control translation. Domain II of the HCV IRES forms a 25-kDa folded subdomain that may alter ribosome conformation. We report here the structure of domain II as determined using an NMR approach that combines short- and long-range structural data. Domain II adopts a distorted L-shape structure, and its overall shape in the free form is markedly similar to its 40S subunit-bound form; this suggests how domain II may modulate 40S subunit conformation. The results show how NMR can be used for structural analysis of large biological RNAs.     

RNA structural motifs: building blocks of a modular biomolecule

RNAs are modular biomolecules, composed largely of conserved structural subunits, or motifs. These structural motifs comprise the secondary structure of RNA and are knit together via tertiary interactions into a compact, functional, three-dimensional structure and are to be distinguished from motifs defined by sequence or function. A relatively small number of structural motifs are found repeatedly in RNA hairpin and internal loops, and are observed to be composed of a limited number of common 'structural elements'. In addition to secondary and tertiary structure motifs, there are functional motifs specific for certain biological roles and binding motifs that serve to complex metals or other ligands. Research is continuing into the identification and classification of RNA structural motifs and is being initiated to predict motifs from sequence, to trace their phylogenetic relationships and to use them as building blocks in RNA engineering.     

Effects of Analogs of the Fungal Sexual Pheromone Sirenin on Male Gamete Motility in Allomyces macrogynus

The ability of various structural analogs of the sexual pheromone sirenin to attract male gametes of the aquatic fungus Allomyces macrogynus was determined. Previous studies had shown that several structural analogs and stereoisomers of natural l-sirenin were devoid of activity at physiological concentrations. We now report the discovery of a structural analog that exhibits biological activity indistinguishable from the natural pheromone. The bioassay system used to determine chemotaxis was calibrated using synthetic, racemic sirenin, which exhibited a threshold concentration for gamete attraction at an applied concentration of 10 picomolar. The new synthetic monohydroxy analog of sirenin also had a threshold concentration of 10 picomolar. In the process of developing a new total synthesis of sirenin, a variety of other analogs were prepared and tested. All of these analogs exhibited threshold concentrations at 1 micromolar or higher, although attraction at these higher concentrations still varied according to their structural resemblance to sirenin. Thus, the results of these studies demonstrate that the hydroxymethyl group attached to the six-membered ring of sirenin is not essential for biological activity at physiological concentrations. The studies with other analogs demonstrate that biological activity at any concentration involves a balance between hydrophilic hydroxyl groups and hydrophobic hydrocarbon groups in the structure.     

Dynamic properties of network motifs contribute to biological network organization

Biological networks, such as those describing gene regulation, signal transduction, and neural synapses, are representations of large-scale dynamic systems. Discovery of organizing principles of biological networks can be enhanced by embracing the notion that there is a deep interplay between network structure and system dynamics. Recently, many structural characteristics of these non-random networks have been identified, but dynamical implications of the features have not been explored comprehensively. We demonstrate by exhaustive computational analysis that a dynamical property—stability or robustness to small perturbations—is highly correlated with the relative abundance of small subnetworks (network motifs) in several previously determined biological networks. We propose that robust dynamical stability is an influential property that can determine the non-random structure of biological networks.     

Synthesis of 5' cap-0 and cap-1 RNAs using solid-phase chemistry coupled with enzymatic methylation by human (guanine-N⁷)-methyl transferase

The 5' end of eukaryotic mRNA carries a N(7)-methylguanosine residue linked by a 5'-5' triphosphate bond. This cap moiety ((7m)GpppN) is an essential RNA structural modification allowing its efficient translation, limiting its degradation by cellular 5' exonucleases and avoiding its recognition as "nonself" by the innate immunity machinery. In vitro synthesis of capped RNA is an important bottleneck for many biological studies. Moreover, the lack of methods allowing the synthesis of large amounts of RNA starting with a specific 5'-end sequence have hampered biological and structural studies of proteins recognizing the cap structure or involved in the capping pathway. Due to the chemical nature of N(7)-methylguanosine, the synthesis of RNAs possessing a cap structure at the 5' end is still a significant challenge. In the present work, we combined a chemical synthesis method and an enzymatic methylation assay in order to produce large amounts of RNA oligonucleotides carrying a cap-0 or cap-1. Short RNAs were synthesized on solid support by the phosphoramidite 2'-O-pivaloyloxymethyl chemistry. The cap structure was then coupled by the addition of GDP after phosphorylation of the terminal 5'-OH and activation by imidazole. After deprotection and release from the support, GpppN-RNAs or GpppN(2'-Om)-RNAs were purified before the N(7)-methyl group was added by enzymatic means using the human (guanine-N(7))-methyl transferase to yield (7m)GpppN-RNAs (cap-0) or (7m)GpppN(2'-Om)-RNAs (cap-1). The RNAs carrying different cap structures (cap, cap-0 or, cap-1) act as bona fide substrates mimicking cellular capped RNAs and can be used for biochemical and structural studies.     

Alternative conformers of 5S ribosomal RNA and their biological relevance

Different conformational states of Escherichia coli 5S ribosomal RNA that may participate in protein biosynthesis have been either detected experimentally or predicted on the basis of phylogenetic sequence comparisons. The A conformer exists in a high-salt form (AH) that binds ribosomal proteins and assembles into the 50S subunit and in a low-salt form (AL), of uncertain biological relevance, that binds at least one ribosomal protein and differs in tertiary structure from the AH form. Experimentally, the AH form has been investigated comprehensively and the AL form partially. There is also a B conformer that exhibits an altered secondary structure and does not assemble with ribosomal proteins. For this conformer exhibits an altered secondary structure and does not assemble with ribosomal proteins. For this conformer to be functionally active, it must be both discrete and universal among 5S RNAs. Here, we examine its structure by employing single and double strand specific ribonucleases and nucleotide-specific chemical reagents. We demonstrate that the B form exhibits a secondary structure only a part of which is both universal and conformationally homogeneous, and we conclude, therefore, that the whole B form cannot participate in protein biosynthesis. We note, however, that progressive structural changes occur during the transitions AH----AL----B and provide evidence that the structural alteration during the transition AH----AL may be universal, which reinforces the view that the AL form is of biological relevance.     

Dissecting NGF interactions with TrkA and p75 receptors by structural and functional studies of an anti-NGF neutralizing antibody

The anti-nerve growth factor (NGF) monoclonal antibody αD11 is a potent antagonist that neutralizes the biological functions of its antigen in vivo. NGF antagonism is expected to be a highly effective and safe therapeutic approach in many pain states. A comprehensive functional and structural analysis of αD11 monoclonal antibody was carried out, showing its ability to neutralize NGF binding to either tropomyosine receptor kinase A (TrkA) or p75 receptors. The 3-D structure of the αD11 Fab fragment was solved at 1.7 Å resolution. A computational docking model of the αD11 Fab-NGF complex, based on epitope mapping using a pool of 44 NGF mutants and experimentally validated by small-angle X-ray scattering, provided the structural basis for identifying the residues involved in αD11 Fab binding. The present study pinpoints loop II of NGF to be an important structural determinant for NGF biological activity mediated by TrkA receptor.     

SWEET-DB: an attempt to create annotated data collections for carbohydrates

Complex carbohydrates are known as mediators of complex cellular events. Concerning their structural diversity, their potential of information content is several orders of magnitude higher in a short sequence than any other biological macromolecule. SWEET-DB (http://www.dkfz.de/spec2/sweetdb/) is an attempt to use modern web techniques to annotate and/or cross-reference carbohydrate-related data collections which allow glycoscientists to find important data for compounds of interest in a compact and well-structured representation. Currently, reference data taken from three data sources can be retrieved for a given carbohydrate (sub)structure. The sources are CarbBank structures and literature references (linked to NCBI PubMed service), NMR data taken from SugaBase and 3D co-ordinates generated with SWEET-II. The main purpose of SWEET-DB is to enable an easy access to all data stored for one carbohydrate structure entering a complete sequence or parts thereof. Access to SWEET-DB contents is provided with the help of separate input spreadsheets for (sub)structures, bibliographic data, general structural data like molecular weight, NMR spectra and biological data. A detailed online tutorial is available at http://www.dkfz.de/spec2/sweetdb/nar/.