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PubMed1987

Structures of human alcohol and aldehyde dehydrogenases.

Human alcohol dehydrogenase is a dimeric zinc metalloenzyme for which forms of three classes, I, II and III, have been distinguished. Subunits hybridize within but not between classes. There are three types of subunit, alpha, beta, and gamma, in class I. The primary structures of all three forms have been established, as well as the overall properties and the effects of the amino acid substitutions between the various forms. Each subunit has 374 residues, of which 35 exhibit differences among the alpha, beta and gamma chains. Corresponding cDNA structures are also known, as are the genetic organization and details of the gene structures. Allelic variants occur at the beta and gamma loci. Corresponding amino acid substitutions have been characterized, and enzymatic differences between the allelic forms are explained by defined residue exchanges. The results also illustrate recent and repeated isozyme evolution, a subject where alcohol dehydrogenases exceptionally well offer detailed examples. Human aldehyde dehydrogenase occurs of two types, a mitochondrial and a cytosolic form. The enzymes are tetramers, do not contain functional metals, and have subunits which do not form inter-type hybrids. The primary structures have been determined, revealing a positional identity of 68% (in 500 residues) between the mitochondrial and cytosolic forms. The N-terminus is heterogeneous and is not blocked in the subunit of the mitochondrial enzyme, in contrast to that of the cytosolic enzyme or those of all the alcohol dehydrogenases (also cytosolic). A reactive cysteine residue at position 302 has been ascribed functional importance at or close to the active site, is conserved in the two aldehyde dehydrogenases, and is associated with the action of disulfiram on the enzyme. In Oriental populations, a mutant allelic variant of the mitochondrial protein with impaired enzyme function has also been characterized.

Alcohol Dehydrogenase↗
PubMed2003

Bridging nonliving and living matter.

Assembling non-biological materials (geomaterials) into a proto-organism constitutes a bridge between nonliving and living matter. In this article we present a simple step-by-step route to assemble a proto-organism. Many pictures have been proposed to describe this transition within the origins-of-life and artificial life communities, and more recently alternative pictures have been emerging from advances in nanoscience and biotechnology. The proposed proto-organism lends itself to both traditions and defines a new picture based on a simple idea: Given a set of required functionalities, minimize the physicochemical structures that support these functionalities, and make sure that all structures self-assemble and mutually enhance each other's existence. The result is the first concrete, rational design of a simple physicochemical system that integrates the key functionalities in a thermodynamically favorable manner as a lipid aggregate integrates proto-genes and a proto-metabolism. Under external pumping of free energy, the metabolic processes produce the required building blocks, and only specific gene sequences enhance the metabolic kinetics sufficiently for the whole system to survive. We propose an experimental implementation of the proto-organism with a discussion of our experimental results, together with relevant results produced by other experimental groups, and we specify what is still missing experimentally. Identifying the missing steps is just as important as providing the road map for the transition. We derive the kinetic and thermodynamic conditions of each of the proto-organism subsystems together with relevant theoretical and computational results about these subsystems. We present and discuss detailed 3D simulations of the lipid aggregation processes. From the reaction kinetics we derive analytical aggregate size distributions, and derive key properties of the metabolic efficiency and stability. Thermodynamics and kinetics of the ligation directed self-replication of the proto-genes is discussed, and we summarize the full life cycle of the proto-organism by comparing size, replication time, and energy with the biomass efficiency of contemporary unicells. Finally, we also compare our proto-organism picture with existing origins-of-life and protocell pictures. By assembling one possible bridge between nonliving and living matter we hope to provide a piece in the ancient puzzle about who we are and where we come from.

Artificial Intelligence↗
PubMed1989

Luminescence and ESR studies of relationships between O(-)-centres and structural iron in natural and synthetically hydrated kaolinites.

Luminescence, induced by dehydration and by wetting with hydrazine and unsymmetrically substituted hydrazine, and related ESR spectra have been observed from several kaolinites, synthetically hydrated kaolinites, and metahalloysites. The amine-wetting luminescence results suggest that intercalation, not a chemiluminescence reaction, is the luminescence trigger. Correlation between hydration-induced luminescence and g = 2 ESR signals associated with O(-)-centres in several natural halloysites, and concurrent diminution of the intensity of both these signal types as a function of aging in two 8.4 angstroms synthetically hydrated, kaolinites, confirm a previously-reported relationship between the luminescence induced by dehydration and in the presence of O(-)-centres (holes, i.e., electron vacancies) in the tetrahedral sheet. Furthermore, the ESR spectra of the 8.4 angstroms hydrate showed a concurrent change in the line shape of the g = 4 signal from a shape usually associated with structural Fe in an ordered kaolinite, to a simpler one typically observed in more disordered kaolinite, halloysite, and montmorillonite. Either structural Fe centres and the O(-)-centres interact, or both are subject to factors previously associated with degree of order. The results question the long-term stability of the 8.4 angstroms hydrate, although XRD does not indicate interlayer collapse over this period. Complex inter-relationships are shown between intercalation, stored energy, structural Fe, and the degree of hydration which may be reflected in catalytic as well as spectroscopic properties of the clays.

Aluminum Silicates↗
PubMed2004

The structurally constrained protein evolution model accounts for sequence patterns of the LbetaH superfamily.

BACKGROUND: Structure conservation constrains evolutionary sequence divergence, resulting in observable sequence patterns. Most current models of protein evolution do not take structure into account explicitly, being unsuitable for investigating the effects of structure conservation on sequence divergence. To this end, we recently developed the Structurally Constrained Protein Evolution (SCPE) model. The model starts with the coding sequence of a protein with known three-dimensional structure. At each evolutionary time-step of an SCPE simulation, a trial sequence is generated by introducing a random point mutation in the current coding DNA sequence. Then, a "score" for the trial sequence is calculated and the mutation is accepted only if its score is under a given cutoff, lambda. The SCPE score measures the distance between the trial sequence and a given reference sequence, given the structure. In our first brief report we used a "global score", in which the same reference sequence, the ancestral one, was used at each evolutionary step. Here, we introduce a new scoring function, the "local score", in which the sequence accepted at the previous evolutionary time-step is used as the reference. We assess the model on the UDP-N-acetylglucosamine acyltransferase (LPXA) family, as in our previous report, and we extend this study to all other members of the left-handed parallel beta helix fold (LbetaH) superfamily whose structure has been determined. RESULTS: We studied site-dependent entropies, amino acid probability distributions, and substitution matrices predicted by SCPE and compared with experimental data for several members of the LbetaH superfamily. We also evaluated structure conservation during simulations. Overall, SCPE outperforms JTT in the description of sequence patterns observed in structurally constrained sites. Maximum Likelihood calculations show that the local-score and global-score SCPE substitution matrices obtained for LPXA outperform the JTT model for the LPXA family and for the structurally constrained sites of class i of other members within the LbetaH superfamily. CONCLUSION: We extended the SCPE model by introducing a new scoring function, the local score. We performed a thorough assessment of the SCPE model on the LPXA family and extended it to all other members of known structure of the LbetaH superfamily.

Acyltransferases↗
PubMed1983

The primary structure of Cu-Zn superoxide dismutase from Photobacterium leiognathi: evidence for a separate evolution of Cu-Zn superoxide dismutase in bacteria.

The complete amino-acid sequence of the copper-zinc superoxide dismutase of the Photobacterium leiognathi was determined. The fragmentation strategy employed included cyanogen bromide cleavage at its methionine residues and the only tryptophan residue. The S-carboxymethylated chain was further cleaved by means of trypsin, in order to obtain overlapping fragments. For sequence determination automated solid or liquid-phase techniques of Edman degradation were used. C-Terminal amino acids of the entire chain were determined after treatment with carboxypeptidase A. Comparison of the primary structure of this bacterial Cu-Zn superoxide dismutase with the established amino-acid sequences of the other eukaryotic Cu-Zn superoxide dismutases revealed clear homologies. Correspondingly, the Cu-Zn-binding amino-acid residues of the active centre were localized: His45, His47, His70, His79, His125 and Asp91. The two cysteine residues in position 52 and 147 were homologous to the cysteine residues, modelling the essential intrachain disulfide bridge of the corresponding bovine enzyme. As only 25-30% of aligned sequence positions were found to be identical, the enzyme of P. leiognathi shows only a remote phylogenetic relationship towards eukaryotic Cu-Zn superoxide dismutases. When compared to the established phylogenetic tree of the cytochrome c family, this indicates a separate evolution of Cu-Zn superoxide dismutase in Photobacterium. Therefore, a natural gene transfer from the eukaryotic host (ponyfish) to the prokaryotic photobacterium, which Martin and Fridovich postulated 1981 (J. Biol. Chem. 256, 6080-6089) on the basis of amino-acid compositions, can be excluded.

Amino Acid Sequence↗
PubMed2005

Mass spectroscopic approach to amino acids formation processes by UV irradiation to simple organic molecules in aqueous solution.

We have studied amino acid formation by UV (193 nm) irradiation to organic molecules (amines, alcohols and amides) in aqueous solution. Among several types of detected amino acids, small aliphatic amino acids (Gly and alpha-, beta-Ala and alpha-, beta-, gamma-ABA) were quantitatively identified. Among these small aliphatic amino acids, certain amino acids were formed in its free form, even before hydrolysis, contrary to the results of UV irradiation to a gas mixture of CO, NH3, and H2O, where amino acids were hardly detected before hydrolysis. The species distribution of identified amino acids showed a dependence on the starting organic molecules, and also on the presence of ammonia. The formation processes of the identified small aliphatic amino acids were investigated with the aid of electrospray ionization (ESI) MS and MS/MS measurements of photoproducts. Possible formation processes of these amino acid precursors from each starting molecules are proposed. By identifying the amino acid precursor, which has a chiral carbon atom, a new possibility is suggested for asymmetric photosynthesis of amino acid from achiral organic molecules.

Amino Acids↗
PubMed1996

[Way to the detection of Mars life].

In this review, I would like to introduce how we can detect the possible life on Mars. Even though the quantitative estimation of the possibility of biogenesis on Mars is difficult, Dr. McKay and his colleagues work has thrown a tiny light for this possibility. Considering Mars environmental conditions, the possible life is microorganisms. The detection of microorganisms in natural environments is not easy even on Earth due to the premature detection technique. We have developed a method based on the fluorescence microscopic technique. This method proved to be successful for the detection of terrestrial microorganisms. Even some pre-biotic cells can be detected. We are developing a miniature detection apparatus which meet the required standard for installing on the Mars landers. We also propose the ground based experiments using Martian meteorites or pseudo-Martian rocks.

Environmental Microbiology↗
PubMed1997

[Pros and cons for Martian life: scientific debate on ALH84001].

Scientific debate related to possible martian life is summarized in this article. Even there is no firm conclusion yet to convince the existence of life on Mars, intensive studies on the meteorite ALH84001 have invoked many valuable findings.

Evolution, Chemical↗
PubMed1998

Abiotic formation of bioorganic compounds in space--preliminary experiments on ground and future exobiology experiments in space.

Simulation experiments on ground have shown that "amino acid precursors", which give amino acids after acid-hydrolysis, can be formed when an ice mixture simulating ice mantles of interstellar dust particles (lSDs) is irradiated with high energy particles or UV light. It is strongly suggested that such bioorganic compounds were delivered by comets for the first biosphere on the Earth. It is of great interest to confirm this hypothesis in actual space conditions, such as in an exposed facility of JEM. Fundamental designs for such exobiology experiments in earth orbit (EEEO) will be discussed.

Amino Acids↗
PubMed1998

From exobiology to cosmobiology at LISA and elsewhere.

Since the emergence of Exobiology, back to the l960ties, this field drastically increased and, although differently named, is today a largely recognized scientific domain of wild interdisciplinarity. It includes not only the search for extraterrestrial living Systems, in particular by direct exploration of planetary bodies and studies of extraterrestrial materials, but also the study on the origins of life on Earth and, in connection to this field, the study of extraterrestrial organic chemistry. The exobiology programmes currently developed at LISA are related to this last aspect. They include the study of prebiotic-like chemistry in the gas and solid phases, based on laboratory simulation experiments, theoretical modeling and future in situ measurements in Titan's atmosphere and in cometary nuclei. A national program of exobiology, coordinated by LISA is under development in France, it covers many of the various aspects of Exobiology, including the study of life in extreme environments, as a reference tool for extraterrestrial life, the study of the primitive environment of the Earth, of the organic chemistry in comets and on Titan, of Mars and Europa and even of extrasolar planets as potential niches for extraterrestrial living systems, associated to the determination of the electromagnetic signatures of life. In parallel to this general program, a proposal for a large simulation chamber to be used as a national facility in particular to simulate the organic chemistry in various planetary environments, and in the interstellar medium, is under preparation. International cooperations linked to these programmes, in particular in the frame of the development of an exobiology facility on the International Space Station, would be of crucial interest.

Atmosphere↗
PubMed1998

Delivery of extraterrestrial amino acids to the primitive Earth. Exposure experiments in Earth orbit.

A large collection of micrometeorites has been recently extracted from Antarctic old blue ice. In the 50 to 100 micrometers size range, the carbonaceous micrometeorites represent 80% of the samples and contain 2% of carbon. They might have brought more carbon to the surface of the primitive Earth than that involved in the present surficial biomass. Amino acids such as "-amino isobutyric acid have been identified in these Antarctic micrometeorites. Enantiomeric excesses of L-amino acids have been detected in the Murchison meteorite. A large fraction of homochiral amino acids might have been delivered to the primitive Earth via meteorites and micrometeorites. Space technology in Earth orbit offers a unique opportunity to study the behaviour of amino acids required for the development of primitive life when they are exposed to space conditions, either free or associated with tiny mineral grains mimicking the micrometeorites. Our objectives are to demonstrate that porous mineral material protects amino acids in space from photolysis and racemization (the conversion of L-amino acids into a mixture of L- and D-molecules) and to test whether photosensitive amino acids derivatives can polymerize in mineral grains under space conditions. The results obtained in BIOPAN-1 and BIOPAN-2 exposure experiments on board unmanned satellite FOTON are presented.

Aluminum Silicates↗
PubMed1998

Evolution of interstellar dust and its relevance to life's origin: laboratory and space experiments.

A scheme is presented for an analog investigation of long term irradiation of ices and organics following the cyclic evolution of interstellar dust. The irradiation is proposed to be performed at cryogenic temperatures on a space platform, and with an enhancement of the solar ultraviolet flux using a concave mirror, grating combination which eliminates the visual and infrared from the sample surface.

Carbon↗
PubMedDate not supplied

Adrenergic receptors: structure and function.

Adrenergic receptors are cell surface glycoproteins that recognize and selectively bind the catecholamines, norepinephrine and epinephrine, which are released from sympathetic nerve endings and the adrenal medulla. By transducing the external catecholamine stimulus into an intracellular signal, these receptors mediate the actions of the sympathetic nervous system, including a variety of responses such as arteriolar smooth muscle contraction and cardiac contraction, while are critically involved in cardiac function and blood pressure homeostasis. Activation or blockade of these receptors is, thus, a major therapeutic approach for the management of a number of cardiovascular disorders, including hypertension, angina pectoris, and cardiac arrhythmias. Additionally, alterations in these receptors or in their coupled intracellular effectors may contribute to or underlie the pathogenesis of cardiovascular diseases such as cardiac hypertrophy, congestive heart failure, and hypertension. Over the past few years, major insights have been gained into the physiology and pharmacology of these receptors, particularly in relationship to the molecular mechanisms involved in their ability to mediate "transmembrane signalling." These insights, which will be reviewed here, have resulted from the isolation and characterization of adrenergic receptors, from the determination of their deduced primary and secondary structures, and from structure-function studies using classical biochemistry and pharmacology as well as recombinant DNA techniques.

Animals↗
PubMedDate not supplied

Probabilities of transversions and transitions.

The values of the mean relative probabilities of transversions and transitions have been refined on the basis of the data collected by Jukes and found to be equal to 0.34 and 0.66, respectively. Evolutionary factors increase the probability of transversions to 0.44. The relative probabilities of individual substitutions have been determined, and a detailed classification of the nonsense mutations has been given. Such mutations are especially probable in the UGG (Trp) codon. The highest probability of AG, GA transitions correlates with the lowest mean change in the hydrophobic nature of the amino acids coded.

Amino Acids↗