Intrapopulational differences of genome structures in two structures of salmon-like fishes

The natural populations of salmon-like catadromous fishes usually include several percents of residual (dwarf) forms, which are 10-15 times smaller than normal forms. A comparative investigation of normal and residual forms in two species: Oncorhynchus nerka and Salvelinus malma (Salmoniformes order) was made by means of DNA molecular hybridization technique. The essential differences in reassociation kinetics was detected in DNA from normal and residual forms of both species. The genome sizes (kinetic complexity) of normal and residual forms are approximately the same. But some families of repetitive nucleotide sequences are represented by considerably different amount of copies. Intrapopulational differences of genome structures of normal and residual forms in both species seem to be more rough in respect to reassociation kinetic than corresponding interspecies differences between malma and nerka. Comparative analyses and reassociation kinetics for long and shrt DNA fragments imply "xenopus type" of nucleotide sequence organization in both species which is common for the majority of animal and plant genomes investigated.     

Prediction of structures of multidomain proteins from structures of the individual domains

We describe the development of a method for assembling structures of multidomain proteins from structures of isolated domains. The method consists of an initial low-resolution search in which the conformational space of the domain linker is explored using the Rosetta de novo structure prediction method, followed by a high-resolution search in which all atoms are treated explicitly and backbone and side chain degrees of freedom are simultaneously optimized. The method recapitulates, often with very high accuracy, the structures of existing multidomain proteins.     

Assembly of protein tertiary structures from secondary structures using optimized potentials

We present a simulated annealing-based method for the prediction of the tertiary structures of proteins given knowledge of the secondary structure associated with each amino acid in the sequence. The backbone is represented in a detailed fashion whereas the sidechains and pairwise interactions are modeled in a simplified way, following the LINUS model of Srinivasan and Rose. A perceptron-based technique is used to optimize the interaction potentials for a training set of three proteins. For these proteins, the procedure is able to reproduce the tertiary structures to below 3 A in root mean square deviation (rmsd) from the PDB targets. We present the results of tests on twelve other proteins. For half of these, the lowest energy decoy has a rmsd from the native state below 6 A and, in 9 out of 12 cases, we obtain decoys whose rmsd from the native states are also well below 5 A.     

Electrodissociation of clathrate-like structures

In the present work, we develop molecular dynamics (MD) simulations in the NPT (isobaric–isothermic) ensemble to analyse the effect of an external electrostatic field over a cubic methane hydrate crystallite. The amplitude of the field is in the range 0.5–3.0 V/nm. For the simulations, we used the SPC/E rigid water model and a single-site model for methane at a temperature of 248 K and a pressure of 20 bar. When the external electrostatic field is applied, the water dipoles are oriented in such a way that the methane molecules can diffuse far away from the water cages, hence the clathrate dissociation takes place. This last phenomenon was observed for intensities above 1.5 V/nm. Taking the final configuration of each run as input, we develop a new set of MD simulations, and we observe that the stable clathrate is not recovered immediately when the external electrostatic field is turned off due to limitations in the simulation time.     

Realization of dependency structures

In this paper we show how to construct block diagram realizations of a given dependency structure and investigate some elementary properties.     

Finite linnaean structures

This paper considers a class of set-theoretical entities, calledn-rank Linnaean structures, which are intended as abstract models of the taxonomic classificatory systems of biology. In the first part, devoted to formalism, finite Linnaean structures are discussed in complete generality; but, in addition, eight distinct subclasses are noted and some of the properties of their elements are explored. In the second part, concerned with applications, it is shown that taxonomic systems may be recast in the form of finite Linnaean structures, and an effort is made to show that some undesirable features of earlier models are avoided without artificiality and without abandoning extensional mathematics.     

Adenovirus complex structures

Adenovirus has, for a long time, been a model system for understanding complex virus structure, assembly and interference in host cell processes. Recent structures of adenoviral capsid proteins critical for cell entry have given new insights into both interactions with host cell receptors and inter-capsid protein interactions, which determine the capsid architecture. Such studies are of importance in engineering adenovirus for use in various gene transfer applications. Remarkable and unexpected similarities have been revealed between the cell-attachment proteins and primary receptors of adenovirus and the unrelated reovirus, and between the capsid proteins and architecture of adenovirus, the enveloped bacteriophage PRD1 and other large DNA viruses.     

Pseudomorphic microbial structures

According to the recent data, carbonaceous chondrites occasionally have pseudomorphoses after microbes. The meteorite ages suggest that life had developed earlier than the Earth was formed.     

Protonated polynucleotide structures

The circular dichroism spectra of poly(dG). poly(dC) have been studied as a function of pH in 0.15 M NaCl solution. Acid titration to pH 2.5 showed two transitions, one around pH 5, the second below pH 3. These transitions are disproportionation reactions and are not due to the dissociation of the complexes. Alkaline back titration to neutrality showed only one step above pH 7, without appearance of the intermediate form. The hysteresis loop observed gave rise to a metastable (probably protonated) form at pH 7 which reverted to the neutral form upon heating or alkali treatment. In order to obtain again the metastable hysteretic form, a whole titration cycle to pH 2.5 had to be performed.Abbreviation CD circular dichroism Dedicated to Prof. A Janke (Vienna) on his 85th birthday.Part 13 is ref. [1].     

Potassium channel structures

The molecular basis of K+ channel function is universally conserved. K+ channels allow K+ flux and are essential for the generation of electric current across excitable membranes. K+ channels are also the targets of various intracellular control mechanisms, such that the suboptimal regulation of channel function might be related to pathological conditions. Because of the fundamental role of K+ channels in controlling membrane excitability, a structural understanding of their function and regulation will provide a useful framework for understanding neuronal physiology. Many recent physiological and crystallographic studies have led to new insights into the workings of K+ channels.     

Modelling molecular structures

This paper gives a guided tour of the teaching programme on molecular modelling offered at the University of Manchester Institute of Science and Technology (UMIST) for first and second-year students. The article describes theory (mini-lectures and self-study projects), and problems that students are expected to tackle at the computer.