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PubMed2006

Principles and applications of GFT projection NMR spectroscopy.

The two defining features of G-matrix Fourier transform (GFT) projection NMR spectroscopy are (i) repeated joint sampling of several indirect chemical shift evolution periods of a multidimensional NMR experiment so that transfer amplitudes are generated which are proportional to all possible permutations of cosine and sine modulations of the individual shifts, and (ii) linear combination of the subspectra resulting from such repeated joint sampling in the time or frequency domain which yields edited subspectra containing signals encoding phase-sensitively detected linear combinations of the jointly sampled shifts. This review sketches the underlying principles of GFT NMR and outlines its relation to further developments such as the reconstruction of multidimensional NMR spectra.

Fourier Analysis↗
PubMed1998

Mechanism and evolution of protein dimerization.

We have investigated the mechanism and the evolutionary pathway of protein dimerization through analysis of experimental structures of dimers. We propose that the evolution of dimers may have multiple pathways, including (1) formation of a functional dimer directly without going through an ancestor monomer, (2) formation of a stable monomer as an intermediate followed by mutations of its surface residues, and (3), a domain swapping mechanism, replacing one segment in a monomer by an equivalent segment from an identical chain in the dimer. Some of the dimers which are governed by a domain swapping mechanism may have evolved at an earlier stage of evolution via the second mechanism. Here, we follow the theory that the kinetic pathway reflects the evolutionary pathway. We analyze the structure-kinetics-evolution relationship for a collection of symmetric homodimers classified into three groups: (1) 14 dimers, which were referred to as domain swapping dimers in the literature; (2) nine 2-state dimers, which have no measurable intermediates in equilibrium denaturation; and (3), eight 3-state dimers, which have stable intermediates in equilibrium denaturation. The analysis consists of the following stages: (i) The dimer is divided into two structural units, which have twofold symmetry. Each unit contains a contiguous segment from one polypeptide chain of the dimer, and its complementary contiguous segment from the other chain. (ii) The division is repeated progressively, with different combinations of the two segments in each unit. (iii) The coefficient of compactness is calculated for the units in all divisions. The coefficients obtained for different cuttings of a dimer form a compactness profile. The profile probes the structural organization of the two chains in a dimer and the stability of the monomeric state. We describe the features of the compactness profiles in each of the three dimer groups. The profiles identify the swapping segments in domain swapping dimers, and can usually predict whether a dimer has domain swapping. The kinetics of dimerization indicates that some dimers which have been assigned in the literature as domain swapping cases, dimerize through the 2-state kinetics, rather than through swapping segments of performed monomers. The compactness profiles indicate a wide spectrum in the kinetics of dimerization: dimers having no intermediate stable monomers; dimers having an intermediate with a stable monomer structure; and dimers having an intermediate with a stable structure in part of the monomer. These correspond to the multiple evolutionary pathways for dimer formation. The evolutionary mechanisms proposed here for dimers are applicable to other oligomers as well.

Biological Evolution↗
PubMed1984

Theoretical investigation of the role of clay edges in prebiotic peptide bond formation. I. Structures of acetic acid, glycine, H2SO4, H3PO4, Si(OH)4, Al(OH)4-.

Activation of amino acids appears to have played a crucial role in prebiotic peptide bond formation. As a model of this process in living systems, phosphates have been used as amino acid activators. The possible role of clay and other minerals has also been investigated. We are presently using ab initio methods to investigate the activation of amino acids by these agents, as an initial step in peptide bond formation. A model of this activation process is described by the reaction: ZCH2COOH + XO4Hn+1 --> ZCH2COOXO3Hn + H2O. The first step in such an investigation, reported here, was to determine the lowest energy structures of a suitable set of reactions. As initial models of amino acids, Z was chosen to be H and NH2, corresponding to acetic acid and glycine, respectively, XO4Hn+1 = H3PO4 represents a phosphate group, while Si(OH)4 describes an edge tetrahedral site of a clay mineral. Al(OH)4- was also included to represent tetrahedral edge site where the silicon is replaced by an aluminum. Finally, to complete the series XO4Hn+1, H2SO4 was added to the set of reactants. All species were optimized using the STO-3G and STO-3G* basis sets. For H3PO4 and Al(OH)4-, STO-3G* full optimizations were not possible. In these cases, certain torsional angles were optimized separately, then held at the optimized value, while the rest of the bond lengths and angles were optimized. All structures were compared to other calculations and to experimental geometries when available.

Acetic Acid↗
PubMed2002

Modelling, steady state analysis and optimization of the catalytic efficiency of the triosephosphate isomerase.

In the present work we have modelled and optimized the reaction mechanism of the triose phosphate isomerase (TIM) enzyme (E.C. 5.3.1.1). For this purpose we have used an approach that combines the S-system representation within the power law formalism and linear programming techniques. By this means we have explored those rate constants whose alterations are likely to improve the catalytic efficiency of the enzyme and investigated the available room for optimization in different metabolic conditions. The role and plausibility of the different types of mutations on the evolution of this enzyme have also been considered. Steady state sensitivity analysis was carried out and a new set of aggregated logarithmic gains was defined in order to quantify the responses of the system to changes in groups of rate constants that could be explained in terms of mutations affecting the catalytic properties of the enzyme. Evaluation of these logarithmic gains at different levels of saturation and disequilibrium ratios enabled us to reach conclusions about the meaning and role of the diffusion limitation terms. The catalytic efficiency of the monoenzymatic system was optimized through changes in the kinetic rate constants within different sets of restrictions ranging from thermodynamic or kinetic to evolutionary ones. Results showed that, at very different conditions, there is still room for improvement in the TIM enzyme. Thus, in a wide range of metabolically significant values of the disequilibrium ratio there is a minimal variation in the optimal profile that yields 2.1 times the velocity of the basal states. Though most of this increase is accounted for by the increase of the second order constants (that could have already reached a theoretical maximum) significant increases (20%) in catalytic efficiencies are obtained by changes of the internal steps only. Besides these new findings our optimization approach has been able to reproduce results obtained with other approaches.

Catalysis↗
PubMed1993

An experimental study of the organic molecules produced in cometary and interstellar ice analogs by thermal formaldehyde reactions.

Thermally promoted formaldehyde (H2CO) reactions in very low temperature ices have been studied to test their importance as a source of organic molecules in astrophysical environments such as comets and interstellar ices. The infrared absorption strengths of a number of the H2CO bands were measured in 10 K ices of pure H2CO and H20:H2CO = 100:3. Infrared spectroscopy was used to monitor the formaldehyde chemistry during warm-up of ices containing H2CO and one or more of the molecules H2O, CH3OH, CO, CO2, O2, and NH3. Formaldehyde reactions do not proceed at low temperatures in the absence of NH3. However, even small traces of NH3 (NH3/H2CO > or = 0.005) are sufficient to induce conversion of a considerable fraction (> 40%) of the H2CO into organic residues. Formaldehyde reactions were observed to start at temperatures as low as 40 K for NH3:H2CO binary ices and at approximately 80 K in astrophysically relevant (i.e., H2O-dominated) ices. A total of five different organic products of these reactions can be distinguished by infrared spectroscopy. One of them is polyoxymethylene (POM), a well-known H2CO polymerization product, whereas the others are reaction products of H2CO with H20, CH3OH and NH3. These all seem to be derivatives of polyoxymethylene. The nature of the components and their relative abundances depend strongly on the initial composition of the ice mixture as well as on the ice's irradiation history. We estimate that about 1% of the organics found in the coma of Comet Halley could have been produced by thermal formaldehyde reactions taking place in the nucleus.

Ammonia↗
PubMed1995

Amino acid racemization on Mars: implications for the preservation of biomolecules from an extinct martian biota.

Using kinetic data, we have estimated the racemization half-lives and times for total racemization of amino acids under conditions relevant to the surface of Mars. Amino acids from an extinct martian biota maintained in a dry, cold (<250 K) environment would not have racemized significantly over the lifetime of the planet. Racemization would have taken place in environments where liquid water was present even for time periods of only a few million years following biotic extinction. The best preservation of both amino acid homochirality and nucleic acid genetic information associated with extinct martian life would be in the polar regions.

Amino Acids↗
PubMed1997

Titan haze: structure and properties of cyanoacetylene and cyanoacetylene-acetylene photopolymers.

The structure and morphological properties of polymers produced photochemically from the UV irradiation of cyanoacetylene and cyanoacetylene mixtures have been examined to evaluate their possible contribution to the haze layers found on Titan. A structural analysis of these polymers may contribute to our understanding of the data returned from the Huygens probe of the Cassini mission that will pass through the atmosphere of Titan in the year 2004. Infrared analysis, elemental analysis, and thermal methods (thermogravimetric analysis, thermolysis, pyrolysis) were used to examine structures of polycyanoacetylenes produced by irradiation of the gas phase HC3N at 185 and 254 nm. The resulting brown to black polymer, which exists as small particles, is believed to be a branched chain of conjugated carbon-carbon double bonds, which, on exposure to heat, cyclizes to form a graphitic structure. Similar methods of analysis were used to show that when HC3N is photolyzed in the presence of Titan's other atmospheric constituents (CH4, C2H6, C2H2, and CO), a copolymer is formed in which the added gases are incorporated as substituents on the polymer chain. Of special significance is the copolymer of HC3N and acetylene (C2H2). Even in experiments where C2H2 was absorbing nearly all of the incident photons, the ratio of C2H2 to HC3N found in the resulting polymer was only 2:1. Scanning electron microscopy was used to visually examine the polymer particles. While pure polyacetylene particles are amorphous spheres roughly 1 micrometer in diameter, polycyanoacetylenes appear to be strands of rough, solid particles slightly smaller in size. The copolymer of HC3N and C2H2 exhibits characteristics of both pure polymers. This is particularly important as pure polyacetylenes do not match the optical constants measured for Titan's atmospheric hazes. The copolymers produced by the incorporation of other minor atmospheric constituents, like HC3N, into the polyacetylenes are expected to have optical constants more comparable to those of the Titan haze.

Acetylene↗
PubMed2000

Prebiotic synthesis of adenine and amino acids under Europa-like conditions.

In order to simulate prebiotic synthetic processes on Europa and other ice-covered planets and satellites, we have investigated the prebiotic synthesis of organic compounds from dilute solutions of NH4CN frozen for 25 years at -20 and -78 degrees C. In addition, the aqueous products of spark discharge reactions from a reducing atmosphere were frozen for 5 years at -20 degrees C. We find that both adenine and guanine, as well as a simple set of amino acids dominated by glycine, are produced in substantial yields under these conditions. These results indicate that some of the key components necessary for the origin of life may have been available on Europa throughout its history and suggest that the circumstellar zone where life might arise may be wider than previously thought.

Adenine↗
PubMed2000

A J-multiplied HMQC (MJ-HMQC) experiment for measuring (3)J(HNHalpha) coupling constants.

The J-multiplied HSQC experiment (MJ-HSQC: S. Heikkinen et al., J. Magn. Reson 137, 243 (1999)) amplifies J coupling constants m times and allows direct observation of the (3)J(HNHalpha) coupling constants of peptides and proteins (<10 kDa). The drawbacks to this method are line broadening in the f(1)-dimension and lower sensitivity. In the J-multiplied HMQC (MJ-HMQC) experiment described here, the PEP-HSQC pulse sequence is replaced by a sensitivity-enhanced HMQC section, and the total decay time for the J-coupling and the chemical shift evolution is shortened by a period of t(1). This experiment affords narrower linewidth and enhances the sensitivity by 34%, on an average of 105 well-isolated peaks, when compared with the MJ-HSQC experiment.

Algorithms↗
PubMed1998

From mineral support to enzymatic catalysis--further assumptions for the evolutionary history of glyoxalase system.

In a previous paper we suggested that the methylglyoxalase pathway might have been an anaplerotic route for the archaic reductive citric acid cycle of surface metabolists at the early stage of evolution. The present paper tries to outline a possible way for the further development of enzyme catalysed glyoxalase path by separating the global process into several plausible evolutionary stages. A sequence of events is proposed which might have led to the emergence of energy rich bonds, especially to the formation of the thiol-ester bond. An explanation is given for the cofactor function of transition metals, as well. A proposition is also made for how nature may preserve molecular mechanisms using them for different purposes if the innovation has proved successful.

Animals↗
PubMed1999

A model of prebiotic replication: survival of the fittest versus extinction of the unfittest.

A model of prebiotic replication discussed by Szathmary and Maynard Smith (1997) is refined in accordance with Lifson's (1997) theory on the crucial stages in the origin of animate matter. The refined model accounts for two processes associated with replication: (1) Replicators always decompose at some rate. (2) Replicators deplete their reactants at a rate equal to the rate of their own replication. Consequently, replicators and their reactants are linked by a non-linear feedback process that keeps them within limits and leads them toward a steady state. The model suggests that: (a) All competing replicators, including those which replicate at sub-exponential "parabolic" and super-exponential "hyperbolic" rates, are subject to natural selection. (b) Survival/extinction is determined by positive/negative net-replication irrespective of the mechanism of replication. (c) Being fit/unfit is the consequence of survival/extinction rather than its cause. In other words, natural selection and survival of the fit is the outcome of continual extinction of the unfit.

Animals↗
PubMed2003

Evolution and function of vitamin D.

It is remarkable that phytoplankton and zooplankton have been producing vitamin D for more than 500 million years. The role of vitamin D in lower non-vertebrate life forms is not well understood. However, it is critically important that most vertebrates obtain an adequate source of vitamin D, either from exposure to sunlight or from their diet, in order to develop and maintain a healthy mineralized skeleton. Vitamin D deficiency is an unrecognized epidemic in most adults who are not exposed to adequate sunlight. This can precipitate and exacerbate osteoporosis and cause the painful bone disease osteomalacia. Once vitamin D is absorbed from the diet or made in the skin by the action of sunlight, it is metabolized in the liver to 25-hydroxyvitamin D [25(OH)D] and then in the kidney to 1,25-dihydroxyvitamin D [1,25(OH)2D]. 1,25(OH)2D interacts with its nuclear receptor (VDR) in the intestine and bone in order to maintain calcium homeostasis. The VDR is also present in a wide variety of other tissues. 1,25(OH)2D interacts with these receptors to have a multitude of important physiological effects. In addition, it is now recognized that many tissues, including colon, breast and prostate, have the enzymatic machinery to produce 1,25(OH)2D. The insights into the new biological functions of 1,25(OH)2D in regulating cell growth, modulating the immune system and modulating the renin-angiotensin system provides an explanation for why diminished sun exposure at higher latitudes is associated with increased risk of dying of many common cancers, developing type 1 diabetes and multiple sclerosis, and having a higher incidence of hypertension. Another calciotropic hormone that is also produced in the skin, parathyroid hormone-related peptide, is also a potent inhibitor of squamous cell proliferation. The use of agonists and antagonists for PTHrP has important clinical applications for the prevention and treatment of skin diseases and disorders of hair growth.

Animals↗
PubMed1999

Formation and processing of organics in the early solar system.

Until pristine samples can be returned from cometary nuclei, primitive meteorites represent our best source of information about organic chemistry in the early solar system. However, this material has been affected by secondary processing on asteroidal parent bodies which probably did not affect the material now present in cometary nuclei. Production of meteoritic organic matter apparently involved the following sequence of events: Molecule formation by a variety of reaction pathways in dense interstellar clouds; Condensation of those molecules onto refractory interstellar grains; Irradiation of organic-rich interstellar-grain mantles producing a range of molecular fragments and free radicals; Inclusion of those interstellar grains into the protosolar nebula with probable heating of at least some grain mantles during passage through the shock wave bounding the solar accretion disc; Agglomeration of residual interstellar grains and locally produced nebular condensates into asteroid-sized planetesimals; Heating of planetesimals by decay of extinct radionuclides; Melting of ice to produce liquid water within asteroidal bodies; Reaction of interstellar molecules, fragments and radicals with each other and with the aqueous environment, possibly catalysed by mineral grains; Loss of water and other volatiles to space yielding a partially hydrated lithology containing a complex suite of organic molecules; Heating of some of this organic matter to generate a kerogen-like complex; Mixing of heated and unheated material to yield the meteoritic material now observed. Properties of meteoritic organic matter believed to be consistent with this scenario include: Systematic decrease of abundance with increasing C number in homologous series of characterisable molecules; Complete structural diversity within homologous series; Predominance of branched-chain isomers; Considerable isotopic variability among characterisable molecules and within kerogen-like material; Substantial deuterium enrichment in all organic fractions; Some fractions significantly enriched in nitrogen-15; Modest excesses of L-enantiomers in some racemisation-resistant molecules but no general enantiomeric preference. Despite much speculation about the possible role of Fischer-Tropsch catalytic hydrogenation of CO in production of organic molecules in the solar nebula, no convincing evidence for such material has been found in meteorites. A similarity between some meteoritic organics and those produced by Miller-Urey discharge synthesis may reflect involvement of common intermediates rather than the operation of electric discharges in the early solar system. Meteoritic organic matter constitutes a useful, but not exact, guide to what we shall find with in situ analytical and sample-return missions to cometary nuclei.

Amino Acids↗
PubMed1979

The mechanical properties of proteins determine the laws of evolutionary change.

The general inorganic nature of traditional selection theory (based on differential growth between any two systems) is pointed out, wherefrom it follows that this theory cannot provide explanations for the characteristics of organic evolution. Specific biophysical aspects enter with the complexity of macro-molecules: vital physical conditions for the perpetuation of the system, irrevocable extinction (= death) and random change leading to novelty, are the result of 'complexity per se'. Further biophysical properties are a direct function of the pathway along which random mutation in nucleic acids is converted into continuous protein - (specifically enzyme) - function, from there into organismic phenotype with fitness components which may, or may not, correspond to identifiable structural units in DNA. The general machine-like properties of enzymes, in that there is no additive relationship between structural (amino acid) composition and functional output, is discussed in more detail. The continuous growth functions of molecular concentrations, directed by enzyme turnover, determine simple laws of growth and morphogenesis in the organic hierarchy and thus of phenotype. Thus, the combined effect of DNA-structure and of environmental parameters (temperature, pressure, pH, etc.) on protein function determines ultimately the actual phenotype and hence, quality and intensity of genotypic selection.

Amino Acids↗