DSMM: a Database of Simulated Molecular Motions

We describe a Database of Simulated Molecular Motions (DSMM). This database is designed to serve as a single searchable site for locating movies and animations from simulations of biomolecules. DSMM is accessible via a webserver at: http://projects.villa-bosch.de/mcm/database/dsmm.     

Superimposing polymorphism: the case of a point mutation within a polymorphic Alu insertion

The COL3A1 Alu insertion is a member of the AluY subfamily. It has been found to be absent in non-human primates and polymorphic in worldwide human populations. The integration of the element into the human genome seems to have preceded the initial migration(s) of anatomically modern humans out of the African continent. Although the insertion has been detected in populations from all the continents, its highest frequency values are located within sub-Saharan Africa. The sequence alignment of the COL3A1 insertion from several African individuals revealed a bi-allelic single nucleotide polymorphism (SNP) at the downstream terminus of the element's poly-A tract. Once discovered, a selective PCR procedure was designed to determine the frequency of both alleles in 19 worldwide populations. The A-allele in this binary SNP experiences a clinal increase in the eastward direction from Africa to Southeast Asia and Mongolia, reaching fixation in the two latter regions. The T variant, on the other hand, exhibits a westward clinal increase outside of Africa, with its lowest frequency in Asia and achieving fixation in northern Europe. The presence of this internal SNP extends the usefulness provided by the polymorphic Alu insertion (PAI). It is possible that superimposing polymorphisms like this one found in the COL3A1 locus may accentuate signals from genetic drift events allowing for visualization of recent dispersal patterns.     

Homozygous nonsense mutations in KIAA1279 are associated with malformations of the central and enteric nervous systems

We identified, by homozygosity mapping, a novel locus on 10q21.3-q22.1 for Goldberg-Shprintzen syndrome (GOSHS) in a consanguineous Moroccan family. Phenotypic features of GOSHS in this inbred family included microcephaly and mental retardation, which are both central nervous system defects, as well as Hirschsprung disease, an enteric nervous system defect. Furthermore, since bilateral generalized polymicogyria was diagnosed in all patients in this family, this feature might also be considered a key feature of the syndrome. We demonstrate that homozygous nonsense mutations in KIAA1279 at 10q22.1, encoding a protein with two tetratrico peptide repeats, underlie this syndromic form of Hirschsprung disease and generalized polymicrogyria, establishing the importance of KIAA1279 in both enteric and central nervous system development.     

Genetic evidence for an interaction between a picornaviral cis-acting RNA replication element and 3CD protein

Internally located, cis-acting RNA replication elements, termed cres, are essential for replication of the genomes of picornaviruses such as human rhinovirus 14 (HRV-14) and poliovirus because they template uridylylation of the protein primer, VPg, by the polymerase 3D(pol). These cres form stem-loop structures sharing a common loop motif, and the HRV-14 cre can substitute functionally for the poliovirus cre in both uridylylation in vitro and RNA replication in vivo. We show, however, that the poliovirus cre is unable to support HRV-14 RNA replication. This lack of complementation maps to the stem of the poliovirus cre and was reversed by single nucleotide substitutions in the stem as well as the base of the loop. Replication-competent, revertant viruses rescued from dicistronic HRV-14 RNAs containing the poliovirus cre, or a chimeric cre containing the poliovirus stem, contained adaptive amino acid substitutions. These mapped to the surface of both the polymerase 3D(pol), at the tip of the "thumb" domain, and the protease 3C(pro), on the side opposing the active site and near the end of an extended strand segment implicated previously in RNA binding. These mutations substantially enhanced replication competence when introduced into HRV-14 RNAs containing the poliovirus cre, and they were additive in their effects. The data support a model in which 3CD or its derivatives 3C(pro) and 3D(pol) interact directly with the stem of the cre during uridylylation of VPg.     

Mutational and structural analysis of stem-loop IIIC of the hepatitis C virus and GB virus B internal ribosome entry sites

Translation of the open reading frames (ORF) of the hepatitis C virus (HCV) and closely related GB virus B (GBV-B) genomes is driven by internal ribosome entry site (IRES) elements located within the 5' non-translated RNA. The functioning of these IRES elements is highly dependent on primary and higher order RNA structures. We present here the solution structures of a common, critical domain within each of these IRESs, stem-loop IIIc. These ten-nucleotide hairpins have nearly identical sequences and similar overall tertiary folds. The final refined structure of each shows a stem with three G:C base-pairs and a novel tetraloop fold. Although the bases are buckled, the first and fourth nucleotides of both tetraloops form a Watson-Crick type base-pair, while the apical nucleotides are located in the major groove where they adopt C(2)-endo sugar puckering with B-form geometry. No hydrogen bonding interactions were observed involving the two apical residues of the tetraloop. Stability of the loops appears to be derived primarily from the stacking of bases, and the hydrogen bonding between the fourth and seventh residues. Mutational analysis shows that the primary sequence of stem-loop IIIc is important for IRES function and that the stem and first and fourth nucleotides of the tetraloop contribute to the efficiency of internal ribosome entry. Base-pair formation between these two positions is essential. In contrast, the apical loop nucleotides differ between HCV and GBV-B, and substitutions in this region of the hairpin are tolerated without major loss of function.     

Acquisition of Hrs, an essential component of phagosomal maturation, is impaired by mycobacteria

Pathogenic mycobacteria survive within macrophages by precluding the fusion of phagosomes with late endosomes or lysosomes. Because the molecular determinants of normal phagolysosome formation are poorly understood, the sites targeted by mycobacteria remain unidentified. We found that Hrs, an adaptor molecule involved in protein sorting, associates with phagosomes prior to their fusion with late endosomes or lysosomes. Recruitment of Hrs required the interaction of its FYVE domain with phagosomal phosphatidylinositol 3-phosphate, but two other attachment sites were additionally involved. Depletion of Hrs by use of small interfering RNA impaired phagosomal maturation, preventing the acquisition of lysobisphosphatidic acid and reducing luminal acidification. As a result, the maturation of phagosomes formed in Hrs-depleted cells was arrested at an early stage, characterized by the acquisition and retention of sorting endosomal markers. This phenotype is strikingly similar to that reported to occur in phagosomes of cells infected by mycobacteria. We therefore tested whether Hrs is recruited to phagosomes containing mycobacteria. Hrs associated readily with phagosomes containing inert particles but poorly with mycobacterial phagosomes. Moreover, Hrs was found more frequently in phagosomes containing avirulent Mycobacterium smegmatis than in phagosomes with the more virulent Mycobacterium marinum. These findings suggest that the inability to recruit Hrs contributes to the arrest of phagosomal maturation induced by pathogenic mycobacteria.     

Hydride complexes of platinum(II) containing unsymmetrical di(phosphine) ligands: synthesis, characterization and evidence for pairwise addition of hydrogen based on parahydrogen induced polarization

Unsymmetrical di(phosphine) ligands (dpp)₂Rop (1a, b = bis(diphenylphosphino)-2-alkyl-3-oxapropane (alkyl = methyl and ethyl)) and (dpp)₂oCy (1c = trans-2-diphenylphosphinocyclohexyl diphenylphosphinite) and their Pt(II) dichloride complexes, PtCl₂((dpp)₂mop) (2a), PtCl₂((dpp)₂eop) (2b) and PtCl₂((dpp)₂oCy) (2c), have been synthesized and characterized by NMR spectroscopy. The crystal structures of 2b and 2c show that the geometry about the platinum centers is square planar. In 2b, the metal and di(phosphine) ligand chelate ring are in a chair conformation, whereas in 2c, the chelate ring conformation is a skewed boat. Initial reaction of sodium borohydride with 2a, b, c yields the monohydride monochloride complexes PtHCl((dpp)₂mop) (5a), PtHCl((dpp)₂eop) (5b) and PtHCl((dpp)₂oCy) (5c). At longer reaction times, fluxional dimeric species are obtained, [PtH((dpp)₂mop)]₂ (4a), [PtH((dpp)₂eop)]₂ (4b) and [PtH((dpp)₂oCy)]₂ (4c),and in the case of 4c two different isomers exist. The dihydride complexes PtH₂((dpp)₂mop) (3a), PtH₂((dpp)₂eop) (3b) and PtH₂((dpp)₂oCy) (3c), are prepared by further reaction of NaBH₄ and 2. Hydrogen cycling is facile in the dihydride complexes 3a, b, c, and oxidative addition of H₂ proceeds in a pairwise manner as determined by the observation of parahydrogen induced polarization (PHIP) in the ¹H NMR spectra. The reductive elimination of H₂ is also shown to be concerted by reaction of dihydride complexes with D₂. Crystal data: 2b (C₃₀H₃₂Cl₆OP₂Pt), monoclinic, space group P2₁/c (No. 14), a = 13.7040(1), b = 11.3430(7), c = 21.3880(9) Å, β = 97.923(9)°, V = 3292.9(2) ų and Z = 4; 2c (C₃₀H₃₀Cl₂OP₂Pt), monoclinic, space group P2₁ (No. 4), a = 11.7360(2), b = 8.4311(2), c = 14.2789(2) Å, β = 101.290(1)°, V = 1385.52(4) ų and Z = 2.     

Human phylogenetic relationships according to the D1S80 locus

By analyzing the allelic frequencies at the D1S80 locus in 43 human populations, we show that the locus is polymorphic globally and that it can be used to discriminate between major racial groups and subpopulations through phylogenetic analysis. Although the use of informative multiple loci generally provides more accurate phylogenetic relationships, in instances where time and/or target DNA availability is limited, D1S80 could provide useful data to discriminate between human groups. Also, knowledge of which loci independently provide accurate phylogenetic relationships, such as the D1S80, can be used to design more accurate multi-locus combinations. In addition, allele frequencies at the locus are reported, for the first time, for Bahamian individuals of African origin and for Chimila, Bari, and Navajo (Cañoncito Valley) native Americans. Allelic data was obtained using standard polymerase chain reaction (PCR) techniques. In the four new populations, 65 genotypes and 20 segregating alleles were observed. All populations conformed to Hardy-Weinberg expectations except the Chimila.