High-resolution structure prediction and the crystallographic phase problem

The energy-based refinement of low-resolution protein structure models to atomic-level accuracy is a major challenge for computational structural biology. Here we describe a new approach to refining protein structure models that focuses sampling in regions most likely to contain errors while allowing the whole structure to relax in a physically realistic all-atom force field. In applications to models produced using nuclear magnetic resonance data and to comparative models based on distant structural homologues, the method can significantly improve the accuracy of the structures in terms of both the backbone conformations and the placement of core side chains. Furthermore, the resulting models satisfy a particularly stringent test: they provide significantly better solutions to the X-ray crystallographic phase problem in molecular replacement trials. Finally, we show that all-atom refinement can produce de novo protein structure predictions that reach the high accuracy required for molecular replacement without any experimental phase information and in the absence of templates suitable for molecular replacement from the Protein Data Bank. These results suggest that the combination of high-resolution structure prediction with state-of-the-art phasing tools may be unexpectedly powerful in phasing crystallographic data for which molecular replacement is hindered by the absence of sufficiently accurate previous models.     

Evidence for the bilobal nature of diferric rabbit plasma transferrin.

Plasma transferrin is involved in iron transport within the circulatory system of vertebrates, and provides an iron source for haemoglobin synthesis and other metabolic requirements. However, despite extensive studies by spectroscopic, biochemical and physiological techniques, the nature of iron binding and the mechanisms of uptake and release of iron are not fully understood. Plasma transferrins are monomeric glycoproteins with a molecular weight of approximately 80,000 (ref. 2); they have two similar and very strong binding sites for Fe(III), together with two associated anion binding sites. Fragmentation studies on various transferrins have shown that the polypeptide chain is composed of two domains formed from the N-terminal and C-terminal halves of the polypeptide chain. Each domain contains one metal binding site. The marked sequence similarities which exist between the two halves may reflect a doubling of an ancestral structural gene during the phylogenetic development of the protein. Preliminary crystallographic investigations of diferric rabbit plasma transferrin have been reported from this laboratory. We now report initial studies of the X-ray structure determination of dife-ric rabbit plasma transferrin which have led to a 6-A resolution electron density map.     

Ab initio determination of solid-state nanostructure

Advances in materials science and molecular biology followed rapidly from the ability to characterize atomic structure using single crystals. Structure determination is more difficult if single crystals are not available. Many complex inorganic materials that are of interest in nanotechnology have no periodic long-range order and so their structures cannot be solved using crystallographic methods. Here we demonstrate that ab initio structure solution of these nanostructured materials is feasible using diffraction data in combination with distance geometry methods. Precise, sub-?ngstr?m resolution distance data are experimentally available from the atomic pair distribution function (PDF). Current PDF analysis consists of structure refinement from reasonable initial structure guesses and it is not clear, a priori, that sufficient information exists in the PDF to obtain a unique structural solution. Here we present and validate two algorithms for structure reconstruction from precise unassigned interatomic distances for a range of clusters. We then apply the algorithms to find a unique, ab initio, structural solution for C60 from PDF data alone. This opens the door to sub-?ngstr?m resolution structure solution of nanomaterials, even when crystallographic methods fail.     

Femtosecond X-ray protein nanocrystallography

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (～200?nm to 2?μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.     

A new approach to protein fold recognition.

The prediction of protein tertiary structure from sequence using molecular energy calculations has not yet been successful; an alternative strategy of recognizing known motifs or folds in sequences looks more promising. We present here a new approach to fold recognition, whereby sequences are fitted directly onto the backbone coordinates of known protein structures. Our method for protein fold recognition involves automatic modelling of protein structures using a given sequence, and is based on the frameworks of known protein folds. The plausibility of each model, and hence the degree of compatibility between the sequence and the proposed structure, is evaluated by means of a set of empirical potentials derived from proteins of known structure. The novel aspect of our approach is that the matching of sequences to backbone coordinates is performed in full three-dimensional space, incorporating specific pair interactions explicitly.     

Three-dimensional structure of an antigen-antibody complex at 6 A resolution

Present understanding of the three-dimensional structure of antibody combining sites is based on X-ray diffraction studies of myeloma immunoglobulins. The structures of the antigen-binding fragment (Fab) complexes of two of these immunoglobulins with small ligands have also been determined. However, there is no crystallographic information concerning the interactions of an antibody with an antigen, nor do we know the precise structure of antigenic determinants on protein molecules. We now report the first structure determination of an antigen-antibody complex at 6 A resolution. The structure of the complex between hen egg-white lysozyme and the Fab of a monoclonal anti-lysozyme antibody (D1.3) shows that the combining site of antibodies is not merely a cleft delineated by the complementarity-determining regions of the variable regions of the light and heavy chains, but is a larger area extending beyond it. A correspondingly large area of the antigen makes close contacts with the antibody, in agreement with the notion of a 'topographical' rather than 'sequential' antigenic determinant. The structural basis of cross-reactivities of an antibody with heterologous antigens and the effect of a single amino acid substitution on antigenic specificity can thus be visualized in the structural model presented here.     

Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy

A half-century after the determination of the first three-dimensional crystal structure of a protein, more than 40,000 structures ranging from single polypeptides to large assemblies have been reported. The challenge for crystallographers, however, remains the growing of a diffracting crystal. Here we report the 4.5-A resolution structure of a 22-MDa macromolecular assembly, the capsid of the infectious epsilon15 (epsilon15) particle, by single-particle electron cryomicroscopy. From this density map we constructed a complete backbone trace of its major capsid protein, gene product 7 (gp7). The structure reveals a similar protein architecture to that of other tailed double-stranded DNA viruses, even in the absence of detectable sequence similarity. However, the connectivity of the secondary structure elements (topology) in gp7 is unique. Protruding densities are observed around the two-fold axes that cannot be accounted for by gp7. A subsequent proteomic analysis of the whole virus identifies these densities as gp10, a 12-kDa protein. Its structure, location and high binding affinity to the capsid indicate that the gp10 dimer functions as a molecular staple between neighbouring capsomeres to ensure the particle's stability. Beyond epsilon15, this method potentially offers a new approach for modelling the backbone conformations of the protein subunits in other macromolecular assemblies at near-native solution states.     

Structure of antibody hypervariable loops reproduced by a conformational search algorithm

The antigen-combining site of antibody molecules consists of six separate loops supported by a conserved beta-sheet framework; antibody specificity arises from length and sequence variation of these 'hypervariable' loops and can be manipulated by transferring sets of loops between different frameworks. Irregular loops are the most difficult parts of protein structure to understand and to model correctly. Here, we describe two computer experiments where all the hypervariable loops were deleted from X-ray structures of mouse immunoglobulins and reconstructed using the conformational search program CONGEN. A protocol was developed for reconstruction of the hypervariable loops in McPC 603 antibody. Calculated loop conformations were generated and a model of the combining site was built from selected low-energy conformations. We then modelled hypervariable loops in another antibody molecule, HyHEL-5. Both models agreed well with the known crystal structures. Our results hold out promise for the success of future modelling studies of complete antigen-combining sites from amino acid sequences.     

Assembly reflects evolution of protein complexes

A homomer is formed by self-interacting copies of a protein unit. This is functionally important, as in allostery, and structurally crucial because mis-assembly of homomers is implicated in disease. Homomers are widespread, with 50-70% of proteins with a known quaternary state assembling into such structures. Despite their prevalence, their role in the evolution of cellular machinery and the potential for their use in the design of new molecular machines, little is known about the mechanisms that drive formation of homomers at the level of evolution and assembly in the cell. Here we present an analysis of over 5,000 unique atomic structures and show that the quaternary structure of homomers is conserved in over 70% of protein pairs sharing as little as 30% sequence identity. Where quaternary structure is not conserved among the members of a protein family, a detailed investigation revealed well-defined evolutionary pathways by which proteins transit between different quaternary structure types. Furthermore, we show by perturbing subunit interfaces within complexes and by mass spectrometry analysis, that the (dis)assembly pathway mimics the evolutionary pathway. These data represent a molecular analogy to Haeckel's evolutionary paradigm of embryonic development, where an intermediate in the assembly of a complex represents a form that appeared in its own evolutionary history. Our model of self-assembly allows reliable prediction of evolution and assembly of a complex solely from its crystal structure.     

The structure of the protein disk of tobacco mosaic virus to 5A resolution.

An electron density map of the TMV disk at 5A resolution has been obtained using isomorphous replacement and non-crystallographic symmetry. The polypeptide chain can be traced with little ambiguity. The axial contacts between protein subunits are unlike those in the virus, the disk being a more open structure apparently designed for rapid interaction with the RNA.     

Hierarchically Clustered HMM for Protein Sequence Motif Extraction with Variable Length

Protein sequence motifs extraction is an important field of bioinformatics since its relevance to the structural analysis. Two major problems are related to this field：（1） searching the motifs within the same protein family; and（2） assuming a window size for the motifs search. This work proposes the Hierarchically Clustered Hidden Markov Model（HC-HMM） approach, which represents the behavior and structure of proteins in terms of a Hidden Markov Model chain and hierarchically clusters each chain by minimizing distance between two given chains＇ structure and behavior. It is well known that HMM can be utilized for clustering, however, methods for clustering on Hidden Markov Models themselves are rarely studied. In this paper, we developed a hierarchical clustering based algorithm for HMMs to discover protein sequence motifs that transcend family boundaries with no assumption on the length of the motif. This paper carefully examines the effectiveness of this approach for motif extraction on 2593 proteins that share no more than 25% sequence identity. Many interesting motifs are generated.Three example motifs generated by the HC-HMM approach are analyzed and visualized with their tertiary structure.We believe the proposed method provides a unique protein sequence motif extraction strategy. The related data mining fields using Hidden Markova Model may also benefit from this clustering on HMM themselves approach.     

Evolutionary information for specifying a protein fold

Classical studies show that for many proteins, the information required for specifying the tertiary structure is contained in the amino acid sequence. Here, we attempt to define the sequence rules for specifying a protein fold by computationally creating artificial protein sequences using only statistical information encoded in a multiple sequence alignment and no tertiary structure information. Experimental testing of libraries of artificial WW domain sequences shows that a simple statistical energy function capturing coevolution between amino acid residues is necessary and sufficient to specify sequences that fold into native structures. The artificial proteins show thermodynamic stabilities similar to natural WW domains, and structure determination of one artificial protein shows excellent agreement with the WW fold at atomic resolution. The relative simplicity of the information used for creating sequences suggests a marked reduction to the potential complexity of the protein-folding problem.     

Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts

Ferritin is important in iron homeostasis. Its twenty-four chains of two types, H and L, assemble as a hollow shell providing an iron-storage cavity. Ferritin molecules in cells containing high levels of iron tend to be rich in L chains, and may have a long-term storage function, whereas H-rich ferritins are more active in iron metabolism. The molecular basis for the greater activity of H-rich ferritins has until now been obscure, largely because the structure of H-chain ferritin has remained unknown owing to the difficulties in obtaining crystals ordered enough for X-ray crystallographic analysis. Here we report the three-dimensional structure of a human ferritin H-chain homopolymer. By genetically engineering a change in the sequence of the intermolecular contact region, we obtained crystals isomorphous with the homologous rat L ferritin and of high enough quality for X-ray diffraction analysis. The X-ray structure of human H ferritin shows a novel metal site embedded within each of its four-helix bundles and we suggest that ferroxidase activity associated with this site accounts for its rapid uptake of iron.     

Transfer of a beta-turn structure to a new protein context

Four-residue beta-turns and larger loop structures represent a significant fraction of globular protein surfaces and play an important role in determining the conformation and specificity of enzyme active sites and antibody-combining sites. Turns are an attractive starting point to develop protein design methods, as they involve a small number of consecutive residues, adopt a limited number of defined conformations and are minimally constrained by packing interactions with the remainder of the protein. The ability to substitute one beta-turn geometry for another will extend protein engineering beyond the redecoration of fixed backbone conformations to include local restructuring and the repositioning of surface side chains. To determine the feasibility and to examine the effect of such a structural modification on the fold and thermodynamic stability of a globular protein, we have substituted a five-residue turn sequence from concanavalin A for a type I' beta-turn in staphylococcal nuclease. The resulting hybrid protein is folded and has full nuclease enzymatic activity but reduced thermodynamic stability. The crystal structure of the hybrid protein reveals that the guest turn sequence retains the conformation of the parent concanavalin A structure when substituted in the nuclease host.     

Polyoma virus capsid structure at 22.5 A resolution

X-ray diffraction data from polyoma capsid crystals were phased by refinement of low-resolution starting models to obtain a self-consistent structural solution. The unexpected result that the hexavalent morphological unit is a pentamer shows that specificity of bonding is not conserved among the protein subunits in the icosahedrally symmetric capsid.     

Structure of the E. coli signal recognition particle bound to a translating ribosome

The prokaryotic signal recognition particle (SRP) targets membrane proteins into the inner membrane. It binds translating ribosomes and screens the emerging nascent chain for a hydrophobic signal sequence, such as the transmembrane helix of inner membrane proteins. If such a sequence emerges, the SRP binds tightly, allowing the SRP receptor to lock on. This assembly delivers the ribosome-nascent chain complex to the protein translocation machinery in the membrane. Using cryo-electron microscopy and single-particle reconstruction, we obtained a 16 A structure of the Escherichia coli SRP in complex with a translating E. coli ribosome containing a nascent chain with a transmembrane helix anchor. We also obtained structural information on the SRP bound to an empty E. coli ribosome. The latter might share characteristics with a scanning SRP complex, whereas the former represents the next step: the targeting complex ready for receptor binding. High-resolution structures of the bacterial ribosome and of the bacterial SRP components are available, and their fitting explains our electron microscopic density. The structures reveal the regions that are involved in complex formation, provide insight into the conformation of the SRP on the ribosome and indicate the conformational changes that accompany high-affinity SRP binding to ribosome nascent chain complexes upon recognition of the signal sequence.     

同源建模方法预测蛋白质突变结构的适用性分析

通过从Protein Data Bank(PDB)结构数据库中提取单氨基酸突变的晶体结构,构建了一组无冗余的测试数据集,对目前应用最广泛的两款同源建模预测软件(SWISS-MODEL和MODELLER)进行了测试分析,发现它们对蛋白质的整体结构预测效果良好,均方根偏差小于0.5埃(RMSD0.5),但在突变导致结构显著变化(RMSD1.5)的情况下却均不能得到准确结果.分类统计显示,发生在蛋白质结构内部和极性氨基酸之间的突变结构变化小,两款软件预测效果较好(RMSD1.0).突变导致结构显著变化的可能性不高(5%),但它对蛋白质功能的影响不可忽视,因此应用同源建模方法对于蛋白质突变的模拟并不完全适用,还需要开发新方法来提高准确性.     

Solving the membrane protein folding problem

One of the great challenges for molecular biologists is to learn how a protein sequence defines its three-dimensional structure. For many years, the problem was even more difficult for membrane proteins because so little was known about what they looked like. The situation has improved markedly in recent years, and we now know over 90 unique structures. Our enhanced view of the structure universe, combined with an increasingly quantitative understanding of fold determination, engenders optimism that a solution to the folding problem for membrane proteins can be achieved.     

三苄基吗啉荒酸基锡的合成及晶体结构研究

以三苄基氯化锡和吗啉荒酸钠为原料,合成了三苄吗啉荒酸基锡.通过X-射线单晶衍射测定了它们的晶体结构.晶体结构为:三斜晶系,空间群P-1,a=0.984 17（16）nm,b=1.081 63（19）nm,c=1.378 8（2）nm,a=72.850（3）°,β=88.895（3）°,γ=64.231（3）°,Z=2,V=1.252 8（4）nm3,Dx=1.469 g/cm3,μ=1.204 mm-1,F（000）=564,R=0.032 8,wR=0.099 5（I≥2σ（I））,对配位中心锡原子而言,属于五配位的扭曲三角双锥结构.