Messages from ultrahigh resolution crystal structures

The ever growing availability of macromolecular crystal structures determined at atomic resolution has now reached a critical size, making it possible to obtain statistically unbiased data on both protein stereochemistry and the validity of the parameters used in their refinement. Besides the determination of the precise geometry of proteins and their active sites, high resolution structures have made it possible to check the application of normal mode calculations, to calculate charge density distributions and to analyze hydration shells around protein molecules. Even if only a few structures involve protein complexes, either with ligands or prosthetic groups, the information obtained in these cases is of great interest for obtaining the physical parameters of these interactions.     

The evolution of the Hox cluster: insights from outgroups

Two burgeoning research trends are helping to reconstruct the evolution of the Hox cluster with greater detail and clarity. First, Hox genes are being studied in a broader phylogenetic sampling of taxa: the past year has witnessed important new data from teleost fishes, onychophorans, myriapods, polychaetes, glossiphoniid leeches, ribbon worms, and sea anemones. Second, commonly accepted notions of animal relationships are being challenged by alternative phylogenetic hypotheses that are causing us to rethink the evolutionary relationships of important metazoan lineages, especially arthropods, annelids, nematodes, and platyhelminthes.     

Pax genes and their roles in cell differentiation and development

Members of the Pax gene family are expressed in various tissues during ontogenesis. Evidence for their crucial role in morphogenesis, organogenesis, cell differentiation and oncogenesis is provided by rodent mutants and human diseases. Additionally, recent experimental in vivo and in vitro approaches have led to the identification of molecules that interact with Pax proteins.     

Chemical approaches toward understanding base excision DNA repair

Despite the importance of DNA repair in protecting the genome, the molecular basis for damage recognition and repair remains poorly understood. In the base excision repair pathway (BER), DNA glycosylases recognize and excise damaged bases from DNA. This review focuses on the recent development of chemical approaches that have been applied to the study of BER enzymes. Several distinctive classes of noncleavable substrate analogs that form stable complexes with DNA glycosylases have recently been designed and synthesized. These analogs have been used for biochemical and structural analyses of protein—DNA complexes involving DNA glycosylases, and for the isolation of a novel DNA glycosylase. An approach to trap covalently a DNA glycosylase-intermediate complex has also been used to elucidate the mechanism of DNA glycosylases.     

Functional genomics: going forwards from the databases

Extrapolating systematically from gene sequence to function is undoubtedly the major challenge facing industry and academia alike as we approach the end of the millennium. Many electronic and laboratory approaches are being developed to meet this challenge but the rate of evolution of these is not keeping pace with the speed of sequence generation.     

Implications of sequencing bacterial genomes for pathogenesis and vaccine development

Improvements in homology search methodology and functional predictions are being complemented by the increase in the volume of sequence data with which comparative analyses can be performed. The experimental methods needed for investigation of gene function and expression in a variety of model systems of infection continue to develop. The identification of surface-exposed microbial structures and their conservation in natural populations of pathogenic species offers prospects for developing novel vaccines. A major challenge is the development of efficient screening methods to select the most promising candidates, such as immunisation with DNA.     

Comparative maps: adding pieces to the mammalian jigsaw puzzle

Comparative maps display the chromosomal location of homologous genes in different species and highlight genetic segments that are conserved in evolution. These maps are used to study chromosomal changes that occurred during the divergence of mammalian lineages, to identify candidates for hereditary disease genes, and to facilitate mapping in other species. Recently, physical mapping in regions of known conserved linkage has revealed previously undetected chromosomal changes that may provide clues to understanding chromosomal structure and function and evolutionary processes. The availability of these data in electronically accessible formats is critical to the growth and analysis of comparative maps.     

A role for the cerebellum in the control of limb movement velocity

Accepting, rejecting or modifying the many different theories of the cerebellum's role in the control of movement requires an understanding of the signals encoded in the discharge of cerebellar neurons and how those signals are transformed by the cerebellar circuitry. Particularly challenging is understanding the sensory and motor signals carried by the two types of action potentials generated by cerebellar Purkinje cells, the simple spikes and complex spikes. Advances have been made in understanding this signal processing in the context of voluntary arm movements. Recent evidence suggests that mossy fiber afferents to the cerebellar cortex are a source of kinematic signals, providing information about movement direction and speed. In turn, the simple spike discharge of Purkinje cells integrates this mossy fiber information to generate a movement velocity signal. Complex spikes may signal errors in movement velocity. It is proposed that the cerebellum uses the signals carried by the simple and complex spike discharges to control movement velocity for both step and tracking arm movements.     

Inertial vestibular coding of motion: concepts and evidence

Central processing of inertial sensory information about head attitude and motion in space is crucial for motor control. Vestibular signals are coded relative to a non-inertial system, the head, that is virtually continuously in motion. Evidence for transformation of vestibular signals from head-fixed sensory coordinates to gravity-centered coordinates have been provided by studies of the vestibulo-ocular reflex. The underlying central processing depends on otolith afferent information that needs to be resolved in terms of head translation related inertial forces and head attitude dependent pull of gravity. Theoretical solutions have been suggested, but experimental evidence is still scarce. It appears, along these lines, that gaze control systems are intimately linked to motor control of head attitude and posture.     

Sialidases: structures, biological significance and therapeutic potential

The structure-based design of a potent inhibitor of the influenza-virus neuraminidase (sialidase) is one of the outstanding successes of rational drug design. Recent clinical trials of the drug have stimulated many companies to seek a share of the potentially huge flu market. Sialidases, however, are involved in the pathogenesis of a whole range of other diseases, so perhaps the knowledge and expertise gained from the influenza story can be used in the design of other drugs, given that they all share certain structural features.     

Bacterial genome sequencing and drug discovery

The availability of bacterial genome sequence information has opened up many new strategies for antibacterial drug hunting. There are obvious benefits for the idetification and evaluation of new drug targets, but genomic-based technology is also beginning to provide new tools for the downstream, preclinical, optimisation of compounds. The greatest benefit from these new approaches lies in the ability to examine the entire genome (or several genomes) simultaneously and in total. In this way, one potential target can be evaluated against another, and either the total effects of functional impairment can be established or the effects of a compound can be compared across species.     

Remembrance of things past: maintaining gene expression patterns with altered chromatin

Eukaryotic organisms have evolved mechanisms to stably preserve the gene expression patterns that determine cell fate. Recent advances have been made in understanding the DNA sequences and protein factors required to propagate gene activation or silencing. These studies suggest that, after gene activity states are selected during development, maintenance protein complexes provide a molecular memory of those states by altering a local domain of chromatin structure.     

The complexities of viral genome analysis: the primate lentiviruses

Analysis of sequence information from RNA-based replication systems continues to challenge the computational molecular biology community. Recent sequence data from the study of primate lentiviruses indicate that extreme sequence heterogeneity, recombination, and cross-species transmissions are all observed in HIV evolution. These types of events will continue to make the development of effective anti-retroviral therapies difficult.     

Coupling cell division and cell death to microtubule dynamics

The mitotic spindle is a self-organizing structure that is constructed primarily from microtubules. Among the most important spindle microtubules are those that bind to kinetochores and form the fibers along which chromosomes move. Chemotherapeutics such as taxol and the vinca alkaloids perturb kinetochore—microtubule attachment and disrupt chromosome segregation. This activates a checkpoint pathway that delays cell cycle progression and induces programmed cell death. Recent work has identified at least four mammalian spindle assembly checkpoint proteins.     

Aminoacyl-tRNA synthetases

Crystallographic studies of a number of aminoacyl-tRNA synthetases and their complexes with ATP, amino acid and cognate tRNA are leading to an increasingly detailed picture of how these sophisticated enzymes function. Within the two distinct structural classes of ten synthetases, many common features are apparent, although evolution has led to many interesting idiosyncrasies in certain enzymes. Recent advances, specially concerning class II enzymes, have increased out knowledge of both the role of electrophiles in the mechanism of amino acid activation and cross-subunit tRNA recognition and help solve the evolutionary puzzles that have emerged from the extension of the aminoacyl-tRNA synthetase database to include Archae     

Everything in moderation: Archaea as ‘non-extremophiles’

Well characterized and cultivated archaea are prokaryotic specialists that thrive in habitats of elevated temperature, low pH, high salinity, or strict anoxia. Recently, however, new groups of abundant, uncultivated archaea have been found to be widespread in more pedestrian biotopes, including marine plankton, terrestrial soils, lakes, marine and freshwater sediments, and in association with metazoa. Research efforts are presently focused on characterizing the physiology, biochemistry and genetics of these abundant and cosmopolitan but poorly understood archaea.     

Asymmetric cell division and cell fate in plants

A variety of approaches has recently been employed to investigate how sister cells adopt distinct fates following asymmetric divisions during plant development. Surgical and drug studies have been used to analyze asymmetric divisions during both early embryogenesis in brown algae and pollen development in tobacco. Genetic screens have been used to identify genes in Arabidopsis thaliana that are required for specific asymmetric cell divisions during pollen and root development. These studies indicate that cell polarity and division orientation are closely tied to the process of cell fate specification, and suggest that differential inheritance of determinants and positional information may both be involved in the specification of cell fates following asymmetric cell division.     

Structure of d-amino acid oxidase: new insights from an old enzyme

d-amino acid oxidase is the prototype of flavin-dependent oxidases. The recent resolution of its 3D structure has provided an explanation for several of its properties and has led to a substantial revision of the mechanism of d-amino acid dehydrogenation, with significant implications for the general uderstanding of flavin-dependent catalysis