Visualizing 3D data obtained from microscopy on the Internet

Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy

We explore structural characterization of protein assemblies by a combination of electron cryo-microscopy (cryoEM) and comparative protein structure modeling. Specifically, our method finds an optimal atomic model of a given assembly subunit and its position within an assembly by fitting alternative comparative models into a cryoEM map. The alternative models are calculated by MODELLER [J. Mol. Biol. 234 (1993) 313] from different sequence alignments between the modeled protein and its template structures. The fitting of these models into a cryoEM density map is performed either by FOLDHUNTER [J. Mol. Biol. 308 (2001) 1033] or by a new density fitting module of MODELLER (Mod-EM). Identification of the most accurate model is based on the correlation between the model accuracy and the quality of fit into the cryoEM density map. To quantify this correlation, we created a benchmark consisting of eight proteins of different structural folds with corresponding density maps simulated at five resolutions from 5 to 15 angstroms, with three noise levels each. Each of the proteins in the set was modeled based on 300 different alignments to their remotely related templates (12-32% sequence identity), spanning the range from entirely inaccurate to essentially accurate alignments. The benchmark revealed that one of the most accurate models can usually be identified by the quality of its fit into the cryoEM density map, even for noisy maps at 15 angstroms resolution. Therefore, a cryoEM density map can be helpful in improving the accuracy of a comparative model. Moreover, a pseudo-atomic model of a component in an assembly may be built better with comparative models of the native subunit sequences than with experimentally determined structures of their homologs.

A cell-centered database for electron tomographic data

Electron tomography is providing a wealth of 3D structural data on biological components ranging from molecules to cells. We are developing a web-accessible database tailored to high-resolution cellular level structural and protein localization data derived from electron tomography. The Cell Centered Database or CCDB is built on an object-relational framework using Oracle 8i and is housed on a server at the San Diego Supercomputer Center at the University of California, San Diego. Data can be deposited and accessed via a web interface. Each volume reconstruction is stored with a full set of descriptors along with tilt images and any derived products such as segmented objects and animations. Tomographic data are supplemented by high-resolution light microscopic data in order to provide correlated data on higher-order cellular and tissue structure. Every object segmented from a reconstruction is included as a distinct entity in the database along with measurements such as volume, surface area, diameter, and length and amount of protein labeling, allowing the querying of image-specific attributes. Data sets obtained in response to a CCDB query are retrieved via the Storage Resource Broker, a data management system for transparent access to local and distributed data collections. The CCDB is designed to provide a resource for structural biologists and to make tomographic data sets available to the scientific community at large.

Bsoft: image and molecular processing in electron microscopy

Software for the processing of electron micrographs in structural biology suffers from incompatibility between different packages, poor definition and choice of conventions, and a lack of coherence in software development. The solution lies in adopting a common philosophy of interaction and conventions between the packages. To understand the choices required to have such common interfaces, I am developing a package called "Bsoft." Its foundations lie in the variety of different image file formats used in electron microscopy-a continually frustrating experience to the user and programmer alike. In Bsoft, this problem is greatly diminished by support for many different formats (including MRC, SPIDER, IMAGIC, SUPRIM, and PIF) and by separating algorithmic issues from image format-specific issues. In addition, I implemented a generalized functionality for reading the tag-base STAR (self-defining text archiving and retrieval) parameter file format as a mechanism to exchanging parameters between different packages. Bsoft is written in highly portable code (tested on several Unix systems and under VMS) and offers a continually growing range of image processing functionality, such as Fourier transformation, cross-correlation, and interpolation. Finally, prerequisites for software collaboration are explored, which include agreements on information exchange and conventions, and tests to evaluate compatibility between packages.

Conformations of the rhodopsin third cytoplasmic loop grafted onto bacteriorhodopsin

BACKGROUND

The third cytoplasmic loop of rhodopsin (Rho EF) is important in signal transduction from the retinal in rhodopsin to its G protein, transducin. This loop also interacts with rhodopsin kinase, which phosphorylates light-activated rhodopsin, and arrestin, which displaces transducin from light-activated phosphorylated rhodopsin.

RESULTS

We replaced eight residues of the EF loop of bacteriorhodopsin (BR) with 24 residues from the third cytoplasmic loop of bovine Rho EF. The surfaces of purple membrane containing the mutant BR (called IIIN) were imaged by atomic force microscopy (AFM) under physiological conditions to a resolution of 0.5-0.7 nm. The crystallinity and extracellular surface of IIIN were not perturbed, and the cytoplasmic surface of IIIN increased in height compared with BR, consistent with the larger loop. Ten residues of Rho EF were excised by V8 protease, revealing helices E and F in the AFM topographs. Rho EF was modeled onto the BR structure, and the envelope derived from the AFM data of IIIN was used to select probable models.

CONCLUSIONS

A likely conformation of Rho EF involves some extension of helices E and F, with the tip of the loop lying over helix C and projecting towards the C terminus. This is consistent with mutagenesis data showing the TTQ transducin-binding motif close to loop CD, and cysteine cross-linking data indicating the C-terminal part of Rho EF to be close to the CD loop.

The BioImage Database Project: organizing multidimensional biological images in an object-relational database

The BioImage Database Project collects and structures multidimensional data sets recorded by various microscopic techniques relevant to modern life sciences. It provides, as precisely as possible, the circumstances in which the sample was prepared and the data were recorded. It grants access to the actual data and maintains links between related data sets. In order to promote the interdisciplinary approach of modern science, it offers a large set of key words, which covers essentially all aspects of microscopy. Nonspecialists can, therefore, access and retrieve significant information recorded and submitted by specialists in other areas. A key issue of the undertaking is to exploit the available technology and to provide a well-defined yet flexible structure for dealing with data. Its pivotal element is, therefore, a modern object relational database that structures the metadata and ameliorates the provision of a complete service. The BioImage database can be accessed through the Internet.

A framework for querying a database for structural information on 3D images of macromolecules: A web-based query-by-content prototype on the BioImage macromolecular server

Nowadays we are experiencing a remarkable growth in the number of databases that have become accessible over the Web. However, in a certain number of cases, for example, in the case of BioImage, this information is not of a textual nature, thus posing new challenges in the design of tools to handle these data. In this work, we concentrate on the development of new mechanisms aimed at "querying" these databases of complex data sets by their intrinsic content, rather than by their textual annotations only. We concentrate our efforts on a subset of BioImage containing 3D images (volumes) of biological macromolecules, implementing a first prototype of a "query-by-content" system. In the context of databases of complex data types the term query-by-content makes reference to those data modeling techniques in which user-defined functions aim at "understanding" (to some extent) the informational content of the data sets. In these systems the matching criteria introduced by the user are related to intrinsic features concerning the 3D images themselves, hence, complementing traditional queries by textual key words only. Efficient computational algorithms are required in order to "extract" structural information of the 3D images prior to storing them in the database. Also, easy-to-use interfaces should be implemented in order to obtain feedback from the expert. Our query-by-content prototype is used to construct a concrete query, making use of basic structural features, which are then evaluated over a set of three-dimensional images of biological macromolecules. This experimental implementation can be accessed via the Web at the BioImage server in Madrid, at http://www.bioimage.org/qbc/index.html.

Design and realization of an on-line database for multidimensional microscopic images of biological specimens

The BioImage database is a new scientific database for multidimensional microscopic images of biological specimens, which is available through the World Wide Web (WWW). The development of this database has followed an iterative approach, in which requirements and functionality have been revised and extended. The complexity and innovative use of the data meant that technical and biological expertise has been crucial in the initial design of the data model. A controlled vocabulary was introduced to ensure data consistency. Pointers are used to reference information stored in other databases. The data model was built using InfoModeler as a database design tool. The database management system is the Informix Dynamic Server with Universal Data Option. This object-relational system allows the handling of complex data using features such as collection types, inheritance, and user-defined data types. Informix datablades are used to provide additional functionality: the Web Integration Option enables WWW access to the database; the Video Foundation Blade provides functionality for video handling.