Correlation of anti-HIV activity with structure: use of electrostatic potential and conformational analysis.

Electrostatic potential distribution, 3-D electron density shapes, and conformational analysis were used to correlate anti-HIV activity or inactivity of AZT, (-) carbovir, oxetanocin A, and 16 isomeric dideoxynucleosides of different families. The structure-activity profile discovered is significant and is expected to contribute to the development of a much needed predictive QSAR analysis in this area.     

Facile cleavage of RNAs by oligoamines. Correlation between amine structure and catalytic activity.

Oligoamines such as ethylenediamine and diethylenetriamine exhibit remarkable catalysis for the hydrolysis of RNAs. Methyl substitution of ethylenediamine at the nitrogen atoms causes virtually no effect on the catalytic activity, indicating that attachment of the oligoamines to sequence-recognizing moiety provides superb artificial ribonuclease.     

Conformations of yeast alpha-mating factor and analog peptides as bound to phospholipid bilayer. Correlation of membrane-bound conformation with physiological activity

The transferred nuclear Overhauser effects of yeast alpha-mating factor [(1-13)peptide] in the presence of various spin-labeled phosphatidylcholines in small unilamellar vesicles of perdeuterated phosphatidylcholine have been analyzed. From the analysis of the quenching effect by spin-labels, the depth of amino acid side chains of the mating factor in phospholipid bilayer has been elucidated. The Leu4 and Leu6 residues are buried deeply in the apolar region of the phospholipid bilayer while the hydrophilic residues such as Gln5 and Lys7 are in the shallow region of the bilayer. The interaction of the side chains of Trp1 and Trp3 residues of alpha-mating factor with the hydrophobic interior of the bilayer contributes to the binding of this peptide with the phosphatidylcholine bilayer. The conformation of des-Trp1-alpha-mating-factor [(2-13)peptide] in the membrane-bound state has been found to be similar to that of (1-13)peptide from the analysis of transferred nuclear Overhauser effects in the presence of mixed vesicles of perdeuterated phosphatidylcholine and perdeuterated phosphatidylserine. The incorporation of this acidic phospholipid in the vesicle remarkably enhances the binding of (1-13)peptide and analog peptides. However, such modifications that weaken the interaction with phospholipid bilayer (deletion of Trp1 and substitution of Trp3 by Gly or Ala) appreciably lower the physiological activity. Transferred nuclear Overhauser effect analyses have also been made of [DHis2]peptide, [DLeu6]peptide and [DLys7]peptide in the presence of the vesicles of perdeuterated phosphatidylcholine. The main-chain conformations of these three analogs in the membrane-bound state have been found to be similar to that of (1-13)peptide, although the side-chain conformations of the D-amino acid residues are naturally different from those of the L-amino acid ones. Thus, the physiological activities of the (1-13)peptide and a variety of analog peptides are found to correlate with the affinities to the phosphatidylcholine/phosphatidylserine membrane and with the molecular conformations in the membrane-bound state.     

Assessment of antimicrobial activity of hydrophilic betaines in osmotically stressed bacteria

A series of hydrophilic aromatic and semi-aromatic betaines related to trigonelline was synthesized and tested for antimicrobial activity. 4-Methylthiazolium betaine was the only one that showed significant antibacterial activity towards Escherichia coli under hyperosmotic conditions. None of the tested betaines showed any evidence of osmoprotection or urea protection. This revised version was published online in June 2006 with corrections to the Cover Date.     

The physiological structure of human C-reactive protein and its complex with phosphocholine.

BACKGROUND: Human C-reactive protein (CRP) is the classical acute phase reactant, the circulating concentration of which rises rapidly and extensively in a cytokine-mediated response to tissue injury, infection and inflammation. Serum CRP values are routinely measured, empirically, to detect and monitor many human diseases. However, CRP is likely to have important host defence, scavenging and metabolic functions through its capacity for calcium-dependent binding to exogenous and autologous molecules containing phosphocholine (PC) and then activating the classical complement pathway. CRP may also have pathogenic effects and the recent discovery of a prognostic association between increased CRP production and coronary atherothrombotic events is of particular interest. RESUTLS: The X-ray structures of fully calcified C-reactive protein, in the presence and absence of bound PC, reveal that although the subunit beta-sheet jellyroll fold is very similar to that of the homologous pentameric protein serum amyloid P component, each subunit is tipped towards the fivefold axis. PC is bound in a shallow surface pocket on each subunit, interacting with the two protein-bound calcium ions via the phosphate group and with Glu81 via the choline moiety. There is also an unexpected hydrophobic pocket adjacent to the ligand. CONCLUSIONS: The structure shows how large ligands containing PC may be bound by CRP via a phosphate oxygen that projects away from the surface of the protein. Multipoint attachment of one planar face of the CRP molecule to a PC-bearing surface would leave available, on the opposite exposed face, the recognition sites for C1q, which have been identified by mutagenesis. This would enable CRP to target physiologically and/or pathologically significant complement activation. The hydrophobic pocket adjacent to bound PC invites the design of inhibitors of CRP binding that may have therapeutic relevance to the possible role of CRP in atherothrombotic events.     

Relationship between osmoprotection and the structure and intracellular accumulation of betaines by Escherichia coli

Abstract Naturally occuring betaines, especially glycine betaine and proline betaine, were accumulated by Escherichia coli from urine. In synthetic hyperosmotic medium, with an homologous series of added betaines, (CH₃)₃N⁺-(CH₂) _n -COO⁻, osmoprotective activity and intracellular accumulation decreased monotonically as n increased from 1 to 5. In contrast, α -substituted glycine betaines were accumulated in a similar manner to glycine betaine, but with different osmoprotective activities. Arsenobetaine, with a quaternary arsonium group, was also accumulated but amino acids which can become negatively charged in a chemically basic environment were not.     

Phosphatidylinositol transfer proteins: structure, catalytic activity, and physiological function

Among the diverse lipid transfer proteins which are found in tissues and biological fluids are those which exhibit a specificity toward phosphatidylinositol and phosphatidylcholine, with a preference for the former. Phosphatidylinositol transfer proteins (PI-TPs) have been purified from several eukaryotic sources; those present in bovine brain and heart have been extensively studied. This review examines the tissue distribution of PI-TPs and the means by which transfer activity is measured using natural and artificial membranes. The interaction of these proteins with lipid monolayers and bilayers is discussed in terms of phospholipid fatty acyl and polar head group compositions. The inhibition of transfer activity by sulfhydryl agents and amphiphilic amines is summarized. The metabolism of the phosphoinositides is considered and a role for PI-TPs is proposed.     

Correlation between structure of polyoxotungstates and their inhibitory activity on polymerases

The 21-tungsto-9-antimonate (TA, HPA 23), a polyoxotungstate, has shown a significant antiviral activity in vivo and in vitro. It inhibits viral and bacterial DNA polymerases. In this paper, several compounds of two polyoxotungstic families, tungstoantimonates and tungstoarsenates, have been used to specify the mechanism of polymerase inhibition. It has been demonstrated that the inhibitory activity of polyoxotungstates is not related to the occupation of their coordinative sites by cations, nor to the nature of these bound cations. Kinetic studies and binding assays have shown that polyoxotungstates bind to the polymerases in competition with the nucleic acid template. This result seems to be related to their polyanionic nature. Furthermore, the size and charge of these compounds may play a prominent part in their affinity for the polymerases.     

Conjugated polyamines and reproductive development: Biochemical, molecular and physiological approaches

Whole tobacco plants containing the root-inducing, left-hand transferred DNA (Ri TL-DNA) display a transformed phenotype, that includes alterations in a number of developmental processes, such as floral induction, flowering and reproduction. We show that the entire Ri TL-DNA is responsible for repression of ornithine and tyrosine decarboxylases while it exerts no effect on transferase and the methyl transferase activities. Evidence is provided that two genes from the Ri TL-DNA, rolA and rolC, alter polyamine metabolism as well as floral induction and flowering. Thus, plants transformed by the rolC gene (under the control of the 35S promoter from cauliflower mosaic virus) were male-sterile (non-viable pollen) and female fertility was reduced by approximatively 80%. A constitutive overexpression of the rolC gene may directly or indirectly cause inhibition of the accumulation of water-insoluble amine conjugates located in the anthers and all the methyl transferases, leading to increases of ornithine decarboxylase, phenylalanine ammonia lyase and putrescine caffeoyl-CoA transferase. The results suggest that male sterility is associated with catabolic processes exerted at the level of water-insoluble amine conjugates and support the view that diamine oxidase may be involved in the regulation of the amine concentration during sexual differentiation, a factor that should be considered when attempting to decipher the mechanisms of control of sexual differentiation. The rolC gene could be useful in determining the role of diamine oxidase in the physiology of flowering. These results suggest that elevated free polyamine and water-soluble polyamine levels (located in the ovaries) contribute to abnormal floral development. The transformed phenotype due to P_35S-rolA(the rolA gene fused to the 35S promoter) consisted of inhibited or delaved flowering, and altered floral morphology in the form of flower abortion. The effects of P_35S-rolA on flowering and fertility are closely correlated with limitations in the accumulation of the water-soluble and -insoluble amine conjugates and increase in accumulation of free amines, indicating that amine conjugates (via transferases) have important functions in floral induction, floral evocation and reproduction. Spermidine availability as well as tyramine availability (in conjugated forms) could be limiting factor(s) in sexual development in tobacco.     

Neuronal activity during spontaneous walking--II. Correlation with stepping

1. During walking in the locust most active brain descending interneurons (DINs) and some from the suboesophageal ganglion (SOG) fire tonically but most SOG DINs show temporally patterned activity. 2. In over half the neurons the temporally patterned firing does not appear to correlate with the stepping cycle. 3. In the remainder, the coincidences with stepping appear to be with particular parts of the step cycle, that is with movement function, rather than with the movement itself. 4. These coincidences or "motor fields" range from the step functions of one leg to a concurrent set of step functions of 3-4 legs, to more than one such set of functions.     

Correlation of structure with transforming activity of the P21 proteins with substitutions at positions 12 and 16

The structural effects of amino acid substitutions at positions 12 and 16 in the amino-terminal segment (Tyr 4-Ala 18) of the ras-oncogene-encoded P21 proteins have been investigated using conformational energy analysis. The P21 protein with Val at position 12 and Lys at position 16 is known to have high transforming ability, while the P21 protein with Val at position 12 and Asn at position 16 is known to have poor transforming ability, similar to that of the normal protein (with Gly at 12 and Lys at 16.) The current results demonstrate a significant conformational change at position 15 induced by the substitution of Asn for Lys at position 16, which could explain this alteration in transformation potential. These findings are consistent with previous results suggesting the existence of a normal and a malignancy-causing conformation for the P21 proteins and suggest that the critical transforming region may encompass residues 12–15.     

Correlation of genomic and physiological traits of thermoanaerobacter species with biofuel yields

Thermophilic anaerobic noncellulolytic Thermoanaerobacter species are of great biotechnological importance in cellulosic ethanol production due to their ability to produce high ethanol yields by simultaneous fermentation of hexose and pentose. Understanding the genome structure of these species is critical to improving and implementing these bacteria for possible biotechnological use in consolidated bioprocessing schemes (CBP) for cellulosic ethanol production. Here we describe a comparative genome analysis of two ethanologenic bacteria, Thermoanaerobacter sp. X514 and Thermoanaerobacter pseudethanolicus 39E. Compared to 39E, X514 has several unique key characteristics important to cellulosic biotechnology, including additional alcohol dehydrogenases and xylose transporters, modifications to pentose metabolism, and a complete vitamin B₁₂ biosynthesis pathway. Experimental results from growth, metabolic flux, and microarray gene expression analyses support genome sequencing-based predictions which help to explain the distinct differences in ethanol production between these strains. The availability of whole-genome sequence and comparative genomic analyses will aid in engineering and optimizing Thermoanaerobacter strains for viable CBP strategies.