The creation of a database of odorous compounds focused on molecular rigidity and analysis of the molecular features of the compounds in the database

It is important to select odorous molecules for experiments on olfaction and for the development of an electronic nose. Odorous molecules having a small number of conformers, namely structurally rigid molecules, are assumed to interact with a small number of types of olfactory receptor proteins or to interact with the proteins in a simpler manner than that of fairly flexible molecules. Focusing on the rigidity of molecular structures, we collected 287 odorous molecules from data sources, which included 1205 chemicals in total and a database of the 287 odorous molecules (DB_odMOL) was created using CS ChemFinder Pro (version 5.0). The logarithmic value of the octanol/water partition coefficient (log P) and melting point, boiling point and vapour pressure of the molecules were estimated using CS Chem3D Pro. The database DB_odMOL accumulates these estimated data in addition to literature values for odour quality, odour detection thresholds and the safety of molecules. The rigidity of the 287 molecules was further analysed by conformational analysis performed by molecular mechanics using Conformer in CS Chem3D Pro (version 5) and 72 rigid odorous molecules were selected. The 287 molecules were also analysed based on atomic composition, substructure and molecular size. Sixty-two odorous molecules among the 72 rigid odorous molecules were further selected based on their atomic composition. The 62 rigid molecules with simple atomic composition that were finally selected should be useful for researchers in choosing odorous molecules for the study of olfaction, including the fields of molecular biology, physiology, structure-odour relationships and other fields of the study concerning odour.     

Mechanism of replication of bacteriophage phi X174 XX. Sensitivity of nascent DNA to single-strand-specific nucleases.

We reported earlier that dephosphorylated nascent phi X174 viral strand DNA molecules were less extensively degraded from the 5' end by spleen exonuclease than were non-nascent molecules. Experiments described here revealed that the insensitivity to the 5'-OH end-specific nuclease was more evident among the longer molecules in the population than among the shorter, all of the molecules being less than unit length in size. The smallest molecules in the population were about as sensitive to the enzyme as the control molecules and hence must possess unblocked 5'-terminal nucleotides. Degradation of the nascent DNA with the 3' end-specific snake venom phosphodiesterase revealed only a small enrichment for [3H]thymidine near the 3' end, seemingly insufficient to account completely for the apparent insensitivity of the longer molecules to spleen exonuclease. When the nascent molecules were isolated without the use of proteolytic enzymes, some pronase-sensitive material was found associated with the DNA, particularly the longer molecules. We suggest that the resistance of the longer nascent (pronase-treated) molecules to spleen exonuclease occurs because they have remnants of the viral gene A or A* protein covalently bound to the 5' end.     

Analysis of CDK2 active-site hydration: a method to design new inhibitors

The interactions between the protein and the solvent were analyzed, and protein regions with a high density of water molecules, as well as structural water molecules, were determined by using molecular dynamics (MD) simulations. A number of water molecules that were in contact with the protein for the whole trajectory were determined. Their interaction energies and hydrogen bonds with protein residues were analyzed. Altogether, 39, 27, 49, and 32 water molecules bound to the protein were found for trajectories of the free CDK2, CDK2/ATP, CDK2/roscovitine, and CDK2/isopentenyladenine complexes, respectively. Positions of observed water molecules were compared with X-ray crystallography data. Special attention was paid to water molecules in the active site of the enzyme, and especially to the deep pocket, where the N9 roscovitine side-chain is buried. Exchange of active-site water molecules with bulk water through the tunnel from the pocket was observed. In the CDK2/isopentenyladenine complex simulation, two water molecules that arrange interaction between the inhibitor and the enzyme via an H-bond were observed. Two stable water molecules in the trajectory of the free CDK2 were found that occupy the same position as the nitrogens N3 and N9 of the isopentenyladenine or N1 and N6 nitrogens of the adenosine triphosphate (ATP). The positions of structural water molecules were compared with the positions of substrate polar groups and crystallographic water molecules found in the Brookhaven Protein Data Bank for various CDK2 complexes. It was concluded that tracing tightly bound water molecules may substantially help in designing new inhibitors.     

Molecular dimensions of the SS and FF phenotypes of human placental alkaline phosphatase: Rotary shadowing and negative staining electron microscope measurements

The two most common homologous phenotypes (SS and FF) of human placental alkaline phosphatase were purified and observed in the electron microscope by rotary shadowing and negative staining techniques. In the rotary shadowing technique, the molecules of the two phenotypes appeared to be approximately elliptical with slit-like structures in the center of the molecules, suggestive of the groove between two subunits. The dimensions of the rotary-shadowed molecules were calculated as 10.1 nm × 5.7 nm for SS and 10.1 nm × 5.6 nm for FF phenotypes. The negative staining technique delivered more fine detail of the molecules than rotary shadowing. The predominant shape of the molecules in this method appeared to be rectangular, with a longitudinal stain-filled groove and with each of the half molecules (presumably 65,000 M_r subunit) very often appearing bi-lobed. This accounts for the molecules which appear to have four pronounced electron-transparent regions. The dimensions of the negatively stained rectangular-shaped molecules were measured as 7.5 nm × 5.5 nm for SS and 7.0 nm × 5.4 nm for FF phenotypes. No significant difference in electron microscopic appearance between the SS and FF phenotypes were observed.     

Ice-water interface migration by temperature controlling for stretching of DNA molecules

This report shows a new DNA stretching method using migration of an ice-water interface. DNA molecules were stretched accompanying the migration of the solid-liquid interface and immobilized in frozen area. This simple method needs no chemical modification to keep DNA in the stretched form. For full stretching of DNA molecules, one terminus of the DNA molecules were anchored on silanized substrate. The anchored DNA molecules were stretched by freezing the DNA solution. The stretched DNA molecules were observed after sublimation of the frozen solution keeping its stretched form on silanized surface which had no attractive interaction with DNA molecules except for the SH-modified terminus in solution. An infrared (IR) laser beam was introduced to a frozen DNA solution through an objective lens for local area melting of the solution. Scanning of the laser irradiation caused stretching and enclosing of DNA molecules in the frozen area followed by migration of the solid-liquid interface.     

Comparative analysis of the structure of double-stranded RNA from killer strains of Saccharomyces cerevisiae

Double-stranded RNAs (M and L molecules) of two strains of the killer system Saccharomyces cerevisiae M437 (wild type) and ski-5 (superkiller mutant) were studied by means of electron microscopy and high resolution thermal melting. The M molecules of the ski-5 mutant were by 100 b.p. shorter than those of M437. L molecules were of the same length for both strains. Analysis of the differential melting curves of L molecules showed that L molecules differ significantly in their nucleotide sequences, whereas M molecules were practically identical. It was found that M molecules contained a long AU region: that of M molecules of M 437 was 170-180 b.p. long and contained almost no GC pairs, whereas the AU region of M molecules of the ski-5 mutant was three times shorter and contained GC pairs.     

Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules

The energetics and hydrogen bonding pattern of water molecules bound to proteins were mapped by analyzing structural data (resolution better than 2.3A) for sets of uncomplexed and ligand-complexed proteins. Water-protein and water-ligand interactions were evaluated using hydropatic interactions (HINT), a non-Newtonian forcefield based on experimentally determined logP(octanol/water) values. Potential water hydrogen bonding ability was assessed by a new Rank algorithm. The HINT-derived binding energies and Ranks for second shell water molecules were -0.04 kcal mol(-1) and 0.0, respectively, for first shell water molecules -0.38 kcal mol(-1) and 1.6, for active site water molecules -0.45 kcal mol(-1) and 2.3, for cavity water molecules -0.55 kcal mol(-1) and 3.3, and for buried water molecules -0.56 kcal mol(-1) and 4.4. For the last four classes, similar energies indicate that internal and external water molecules interact with protein almost equally, despite different degrees of hydrogen bonding. The binding energies and Ranks for water molecules bridging ligand-protein were -1.13 kcal mol(-1) and 4.5, respectively. This energetic contribution is shared equally between protein and ligand, whereas Rank favors the protein. Lastly, by comparing the uncomplexed and complexed forms of proteins, guidelines were developed for prediction of the roles played by active site water molecules in ligand binding. A water molecule with high Rank and HINT score is unlikely to make further interactions with the ligand and is largely irrelevant to the binding process, while a water molecule with moderate Rank and high HINT score is available for ligand interaction. Water molecule displaced for steric reasons were characterized by lower Rank and HINT score. These guidelines, tested by calculating HINT score and Rank for 50 water molecules bound in the active site of four uncomplexed proteins (for which the structures of the liganded forms were also available), correctly predicted the ultimate roles (in the complex) for 76% of water molecules. Some failures were likely due to ambiguities in the structural data.     

Atomic force microscopy-based detection of binding and cleavage site of matrix metalloproteinase on individual type II collagen helices

Type II tropocollagen molecules were reacted with matrix metalloproteinase 8 (MMP-8) and the binding sites as well as the cleavage site of MMP-8 were detected on individual molecules using atomic force microscopy (AFM). Approximately 300-nm-long coiled-coil tropocollagen molecules were straightened and immobilized on an atomically flat surface for detection by AFM. The direct visualization of individual collagen molecules revealed heterogeneous characteristics of MMP-8:collagen complexes. We observed that there existed multiple MMP-8 nonspecific binding sites on the collagen molecules, but cleavage always took place at a unique site. When collagen molecules, straightened and immobilized on the surface, were reacted with MMP-8, a site of cleavage appeared as a gap in stretched molecules. This is the first report to visually show direct collagenase:collagen interactions using AFM. The described AFM-based analysis has potential as a protein analysis tool for understanding a complex mechanism of enzyme:substrate interactions.     

MHC-like molecules in some nonmammalian vertebrates can be detected by some cross-reactive monoclonal antibodies.

mAb to human and mouse MHC molecules were tested for binding to blood or spleen cells of various nonmammalian vertebrates by immunofluorescence and flow cytometry. Those that bound were used to immunoprecipitate cross-reactive molecules from biosynthetically or cell surface-labeled spleen or blood cells. In addition, mAb to human MHC molecules were screened by Western blots. As expected from the results with xenoantisera, there were few mAb that cross-reacted, and many of these cross-reactions were not specific for MHC-like molecules. Less than 10% of the mAb tested bound to the cells of any particular species, with very few positive for more than one species. Of those mAb that bound cells, many failed to precipitate any radioactive bands, and most bands precipitated were not recognizable as MHC-like molecules. Five mAb reacted with Xenopus class II, one of which also immunoprecipitated axolotl class II. Another of these reacted with a candidate for class II in the lamprey, but this molecule had features unlike those expected for mammalian class II molecules. Four other mAb reacted with candidate molecules. in the trout and shark. None of the mouse alloantibodies immunoprecipitated nonmammalian vertebrate MHC-like molecules. In contrast to the results with most xenoantisera, the mAb cross-reacting with amphibian class II molecules recognized a number of different linear epitopes on the surface of the polymorphic non-Ig beta 1 domain of class II molecules. Few mAb recognized bands in Western blots of nonmammalian vertebrate cells and the candidate molecules from fish had features different from known mammalian MHC molecules.     

Electron microscopical localization of the alpha 2-macroglobulin thiol ester sites

The active thiol ester groups of alpha 2-macroglobulin (alpha 2M) were reacted with a biotin derivative and the sites labelled with avidin-ferritin complexes. Electron micrographs show a strong preference of attachment of the ferritins to the ends of the rods of the H-shaped molecules. A mutual "cross-labelling" was observed in an alpha 2M preparation which yielded dimers of the molecules which must have been formed during purification. The molecules were mostly attached to each other at the ends of the rods of the H-shaped molecules. It is concluded that the thiol esters responsible for the covalent attachment of the proteinases (and other molecules) may be located more in the distal parts of the alpha 2M molecules, while the proteinase molecules are finally trapped near to the centre of the alpha 2M molecules.     

Heavy chain variable region allotypic sub-specificities of rabbit immunoglobulins. I. Identification of three subpopulations of a1 IgG molecules.

Four anti-al Ab subpopulations were isolated from an anti-al antiserum by sequential immunoadsorption chromatography. These four anti-al Ab subpopulations were differentially bound by two "limited heterogeneity" Abs having different components of the al allotypic specificity. Each of the four anti-al Ab subpopulations reacted with al IgG molecules obtained from a2 and a3 rabbits. A subpopulation designated anti-al Ab reacted with 100% of al IgG molecules. Thus, the anti-al-A Ab recognizes al determinants common to all al IgG molecules. Each of the other three subpopulations, designated anti-al-B Ab, anti-al-C Ab, and anti-al-D Ab, reacted with only a fraction of the al IgG molecules but the sum of the percentages of al IgG molecules which reacted with each of these three anti-al Ab subpopulations approximated 100% of the al IgG molecules. Thus each of the anti-al-B Ab, anti-al-C Ab, and anti-al-D Ab recognizes non-common determinants distinct for each of three subpopulations of al IgG molecules. Although 65 to 90% of IgG molecules in al homozygous rabbits have the al allotypic specificity, these IgG molecules are heterogeneous with respect to their antigenic determinants comprising the al allotype; at least three kinds of al IgG molecules are identified. This heterogeneity probably reflects variation in the amino acid sequence of the Vh region of al IgG molecules and, therefore, poses a similar argument which had led to the hypothesis of two genes for one polypeptide chain and to the theory of episomal insertions for the genetic control of immunoglobulin synthesis.     

Double labelling of major histocompatability complex molecules and lysosomal protein lamp-1 on human dendritic cells

Summary In this study, double labelling for major histocompatability complex (MHC) class I and class II molecules and for MHC molecules and the lysosomal membrane protein lamp-1 on ultrathin cryosections of dendritic cells isolated from human peripheral blood was performed. The plasma membrane proved to be positive for both MHC class I and MHC class II molecules and was labelled for only a very few lamp-1 molecules. MHC class I and MHC class II molecules did not co-localize intracellularly except in some peripherally located vesicles. However, many MHC class II-labelled vesicles were present in a juxtanuclear position but only some of them were co-labelled for lamp-1. These results indicate the presence of a separate, non-lysosomal compartment for class II molecules in dendritic cells.     

The Robustness of Naturally and Artificially Selected Nucleic Acid Secondary Structures

Thermodynamic stability and mutational robustness of secondary structure are critical to the function and evolutionary longevity of RNA molecules. We hypothesize that natural and artificial selection for functional molecules favors the formation of structures that are stable to both thermal and mutational perturbation. There is little direct evidence, however, that functional RNA molecules have been selected for their stability. Here we use thermodynamic secondary structure prediction algorithms to compare the thermal and mutational robustness of over 1000 naturally and artificially evolved molecules. Although we find evidence for the evolution of both types of stability in both sets of molecules, the naturally evolved functional RNA molecules were significantly more stable than those selected in vitro, and artificially evolved catalysts (ribozymes) were more stable than artificially evolved binding species (aptamers). The thermostability of RNA molecules bred in the laboratory is probably not constrained by a lack of suitable variation in the sequence pool but, rather, by intrinsic biases in the selection process.     

Role of interstellar molecules in prebiological evolution

Three generations of organic molecules in space are considered: interstellar molecules, molecules synthesised in protosolar cloud and molecules synthesised on the Earth. It is shown that there is no possibilities for amino acid polymers to be synthesised under interstellar cloud conditions. Molecules of the second generation were disintegrated during the Earth accumulation period. The problem of the origin of life is connected with the evolution of molecules of the third generation.     

Endocytosis and recycling of MHC-encoded class II molecules by mouse B lymphocytes

The movements of mouse MHC-encoded class II (H-2E) and class I (H-2K), transferrin receptor and surface Ig molecules of B lymphocytes were studied using radiolabeled mAb and electron microscopy. A total of 10 to 20% of antibodies specific for H-2E molecules were gradually internalized with a t 1/2 of 15 min, reaching a plateau after 30 min at 37 degrees C. Equivalent results were obtained either with the whole antibody or Fab' fragments, suggesting that the internalization of class II molecules was spontaneous. Similar results were obtained with antibodies specific for the transferrin receptor, of which 50% were internalized with t 1/2 of 5 min, reaching a plateau after 30 min. In contrast to antibodies specific for H-2E molecules and the transferrin receptor, antibodies specific for H-2K were not internalized. Reappearance of internalized H-2E-specific antibodies at the cell surface was observed at 37 degrees C. When compared to antibodies specific for surface Ig, degradation of antibodies specific for H-2E molecules was limited even after 5 h incubation. Neither ammonium chloride nor cycloheximide inhibited internalization and recycling. Electron microscopy showed that internalization of H-2E molecules occurred via coated pits/coated vesicles. These results indicate that class II molecules are spontaneously internalized and recycled by B lymphocytes.     

Genetic transformation of Saccharomyces cerevisiae with single-stranded circular DNA vectors

We asked if single-stranded vector DNA molecules could be used to reintroduce cloned DNA sequences into a eukaryotic cell and cause genetic transformation typical of that observed using double-stranded DNA vectors. DNA was presented to Saccharomyces cerevisiae following a standard transformation protocol, genetic transformants were isolated, and the physical state of the transforming DNA sequence was determined. We found that single-stranded DNA molecules transformed yeast cells 10- to 30-fold more efficiently than double-stranded molecules of identical sequence. More cells were competent for transformation by the single-stranded molecules. Single-stranded circular (ssc) DNA molecules carrying the yeast 2 μ plasmid-replicator sequence were converted to autonomously replicating double-stranded circular (dsc) molecules, suggesting their efficient utilization as templates for DNA synthesis in the cell. Single-stranded DNA molecules carrying 2 μ plasmid non-replicator sequences recombined with the endogenous multicopy 2 μ plasmid DNA. This recombination yielded either the simple molecular adduct expected from homologous recombination (40% of the transformants examined) or aberrant recombination products carrying incomplete transforming DNA sequences, endogenous 2 μ plasmid DNA sequences, or both (60% of the transformants examined). These aberrant recombination products suggest the frequent use of a recombination pathway that trims one or both of the substrate DNA molecules. Similar aberrant recombination products were detected in 30% of the transformants in cotransformation experiments employing single-stranded and double-stranded DNA molecules, one carrying the 2 μ plasmid replicator sequence and the other the selectable genetic marker. We conclude that single-stranded DNA molecules are useful vectors for the genetic transformation of a eukaryotic cell. They offer the advantage of high transformation efficiency, and yield the same intracellular DNA species obtained upon transformation with double-stranded DNA molecules. In addition, single-stranded DNA molecules can participate in a recombination pathway that trims one or both DNA recombination substrates, a pathway not detected, at least at the same frequency, when transforming with double-stranded DNA molecules     

Topological linkage of circular DNA molecules promoted by Ustilago rec 1 protein and topoisomerase

We studied the formation of linked circular DNA molecules promoted by the combined action of rec 1 protein and type I topoisomerase of Ustilago maydis. When ATP was added as cofactor to reactions containing rec 1 protein, pairs of homologous circular DNA molecules became linked after addition of topoisomerase. Closed circular duplex molecules could be joined at homologous sites with circular single-stranded molecules or with other circular duplex molecules, provided that homologous single-stranded DNA fragments or RNA polymerase and nucleoside triphosphates were also added. Complexes formed were topologically linked through regions of heteroduplex DNA. When the analog adenylyl-imidodiphosphate was substituted for ATP, nonhomologous pairs of circular DNA molecules became linked.     

Actin Associates with the Nucleocapsid Domain of the Human Immunodeficiency Virus Gag Polyprotein

Recently, it was shown that actin molecules are present in human immunodeficiency virus type 1 (HIV-1) particles. We have examined the basis for incorporation and the location of actin molecules within HIV-1 and murine retrovirus particles. Our results show that the retroviral Gag polyprotein is sufficient for actin uptake. Immunolabeling studies demonstrate that actin molecules localize to a specific radial position within the immature particle, clearly displaced from the matrix domain underneath the viral membrane but in proximity to the nucleocapsid (NC) domain of the Gag polyprotein. When virus or subviral Gag particles were disrupted with nonionic detergent, actin molecules remained associated with the disrupted particles. Actin molecules remained in a stable complex with the NC cleavage product (or an NC-RNA complex) after treatment of the disrupted HIV-1 particles with recombinant HIV-1 protease. In contrast, matrix and capsid molecules were released. The same result was obtained when mature HIV-1 particles were disrupted with detergent. Taken together, these results indicate that actin molecules are associated with the NC domain of the viral polyprotein.     

Molecular docking of azole drugs and their analogs on CYP121 of Mycobacterium tuberculosis

The Mycobacterium tuberculosis genome codes for 20 different cytochromes. These cytochromes are involved in the breakdown of recalcitrant pollutants and the synthesis of polyketide antibiotics and other complex macromolecules. It has been demonstrated that CYP121 is essential for viability of the bacterium by gene knock-out and complementation studies. CYP121 could therefore be a probable target for the development of new drugs for TB. It has been widely reported that orthologs of CYP121 in fungi are inhibited by azole drugs. We evaluated whether these azole drugs or their structural analogs could bind to and inhibit CYP121 of M. tuberculosis using molecular docking. Six molecules with known anti-CYP121 activity were selected from literature and PubChem database was searched to identify structural analogs for these inhibitors. Three hundred and fifty seven molecules were identified as structural analogs and used in docking studies. Fifty three molecules were found to be scored better than the azole drugs and five of them were ranked among the top 12 molecules by two different scoring functions. These molecules may be further tested by in vitro experimentation for their activity against CYP121 of M. tuberculosis.     

The biosynthetic pathway of MHC class II but not class I molecules intersects the endocytic route

We studied the intracellular traffic and subcellular distribution of MHC class I and class II antigens in comparison with a recycling surface glycoprotein, the transferrin receptor (Tfr), in the human lymphoblastoid cell line JY. No internalization was detectable for class I molecules. Class II molecules were internalized but did not recycle. In contrast, Tfr was found to internalize and recycle. The biosynthetic pathway of class II molecules differ from that of class I molecules in that it shows a delay (1-3 hr) in transport from trans-Golgi to cell surface: here it intersects the endocytic route. Immunoelectron microscopy using anti-MHC antibodies revealed the existence of vesicular structures that were intensely labeled for class II molecules. It is proposed that at this site combination of class II molecules with processed antigen could occur.