Hemifacial microsomia. Etiology, diagnosis and treatment.

BACKGROUND: Three percent of all newborns have significant structural anomalies. Hemifacial microsomia, or HFM, is the second most common facial anomaly, second only to cleft lip and palate. New therapeutic and clinical management techniques offer promising interventions that can allow many patients to have more normal childhoods at earlier ages. DESCRIPTION: Due to a unilateral deficiency of the mandible and lower face, patients who have HFM have specific dental needs that require restorative, orthodontic and surgical correction. CLINICAL IMPLICATIONS: Oral and maxillofacial malformations present diagnostic and treatment challenges unique to the dental profession. The etiology, diagnosis and treatment modalities discussed in this article can be used to help effectively rehabilitate patients who have HFM.

Genome of the bacterium Streptococcus pneumoniae strain R6.

Streptococcus pneumoniae is among the most significant causes of bacterial disease in humans. Here we report the 2,038,615-bp genomic sequence of the gram-positive bacterium S. pneumoniae R6. Because the R6 strain is avirulent and, more importantly, because it is readily transformed with DNA from homologous species and many heterologous species, it is the principal platform for investigation of the biology of this important pathogen. It is also used as a primary vehicle for genomics-based development of antibiotics for gram-positive bacteria. In our analysis of the genome, we identified a large number of new uncharacterized genes predicted to encode proteins that either reside on the surface of the cell or are secreted. Among those proteins there may be new targets for vaccine and antibiotic development.

Adduct formation between alkali metal ions and divalent metal salicylaldimine complexes having methoxy substituents. A structural investigation.

Sodium, potassium, and cesium salts (iodides, nitrates, acetates, and tetraphenylborates) form 1/1, 1/2 and 2/3 adducts with MLn [M = Co, Ni, Cu, and Zn; n = 1-4; H2L1 = N,N'-(3-methoxysalicyliden)ethane-1,2-diamine; H2L2, H2L3, and H2L4 are the -propane-1,2-diamine, -o-phenylenediamine, and -propane-1,3-diamine analogues of H2L1). Metal salicyladimine, alkali metal, and anion all exert influence on stoichiometry and reactivity. Sodium ions tend to reside within the planes of the salicylaldimine oxygens, as in Na(NO3)(MeOH).NiL4 (1), Na(NO3)(MeOH).CuL1 (2; both with unusual seven-coordinated sodium), and Na.(NiL4)2I.EtOH.H2O (3; with dodecahedral sodium coordination geometry). Potassium and cesium tend to locate between salicylaldimine ligands as in KI.NiL4 (4) and [Cs(NO3).NiL4]3.MeOH (5; structures with infinite sandwich assemblies), CsI.(NiL2)2.H2O (6), CsI3.(NiL4)2 (7; simple sandwich structures), and [K(MeCN)]2.(NiL4)3 (8; a triple-decker sandwich structure). Crystal data for 1 are the following: triclinic, P1, a = 7.3554(6) A, b = 11.2778(10) A, c = 13.562(2) A, alpha = 96.364(10) degrees, beta = 101.924(9) degrees, gamma = 96.809(10) degrees, Z = 2. For 2, triclinic, P1, a = 7.2247(7) A, b = 11.0427(6) A, c = 13.5610(12) A, alpha = 94.804(5) degrees, beta = 98.669(7) degrees, gamma = 99.26(6) Z = 2. For 3, orthorhombic, Pbca, a = 14.4648(19) A, b = 20.968(3) A, c = 28.404(3) A, Z = 8. For 4, triclinic, P1, a = 12.4904(17) A, b = 13.9363(13) A, c = 14.1060(12) A, alpha = 61.033(7) degrees, beta = 89.567(9) degrees, gamma = 71.579(10) degrees, Z = 2. For 5, monoclinic. P2(1)/n, a = 12.5910(2) A, b = 23.4880(2) A, c = 22.6660(2) A, beta = 99.3500(1) degree, Z = 4. For 6, orthorhombic, Pbca, a = 15.752(3) A, b = 23.276(8) A, c = 25.206(6) A, Z = 8. For 7, triclinic, P1, a = 9.6809(11) A, b = 10.0015(13) A, c = 11.2686(13) A, alpha = 101.03 degrees, beta = 90.97 degrees, gamma = 100.55 degrees, Z = 2. For 8, monoclinic, C2/c, a = 29.573(5) A, b = 18.047(3) A, c = 23.184(3) A, beta = 122.860(10) degrees, Z = 8.

Structure of a binary complex of HhaI methyltransferase with S-adenosyl-L-methionine formed in the presence of a short non-specific DNA oligonucleotide.

We have determined a structure for a complex formed between HhaI methyltransferase (M.HhaI) and S-adenosyl-L-methionine (AdoMet) in the presence of a non-specific short oligonucleotide. M.HhaI binds to the non-specific short oligonucleotides in solution. Although no DNA is incorporated in the crystal, AdoMet binds in a primed orientation, identical with that observed in the ternary complex of the enzyme, cognate DNA, and AdoMet or S-adenosyl-L-homocysteine (AdoHcy). This orientation differs from the previously observed unprimed orientation in the M.HhaI-AdoMet binary complex, where the S+-CH3 unit of AdoMet is protected by a favorable cation-pi interaction with Trp41. The structure suggests that the presence of DNA can guide AdoMet into the primed orientation. These results shed new light on the proposed ordered mechanism of binding and explains the stable association between AdoMet and M.HhaI.

Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine.

A key step in the predicted mechanism of enzymatic transfer of methyl groups from S-adenosyl-l-methionine (AdoMet) to cytosine residues in DNA is the transient formation of a dihydrocytosine intermediate covalently linked to cysteine in the active site of a DNA (cytosine C5)-methyltransferase (DNA C5-MTase). Crystallographic analysis of complexes formed by HhaI methyltransferase (M.HhaI), AdoMet and a target oligodeoxyribonucleotide containing 5-fluorocytosine confirmed the existence of this dihydrocytosine intermediate. Based on the premise that 5,6-dihydro-5-azacytosine (DZCyt), a cytosine analog with an sp3-hybridized carbon (CH2) at position 6 and an NH group at position 5, could mimic the non-aromatic character of the cytosine ring in this transition state, we synthesized a series of synthetic substrates for DNA C5-MTase containing DZCyt. Substitution of DZCyt for target cytosines in C-G dinucleotides of single-stranded or double-stranded oligodeoxyribonucleotide substrates led to complete inhibition of methylation by murine DNA C5-MTase. Substitution of DZCyt for the target cytosine in G-C-G-C sites in double-stranded oligodeoxyribonucleotides had a similar effect on methylation by M. HhaI. Oligodeoxyribonucleotides containing DZCyt formed a tight but reversible complex with M.HhaI, and were consistently more potent as inhibitors of DNA methylation than oligodeoxyribonucleotides identical in sequence containing 5-fluorocytosine. Crystallographic analysis of a ternary complex involving M.HhaI, S-adenosyl-l-homocysteine and a double-stranded 13-mer oligodeoxyribonucleotide containing DZCyt at the target position showed that the analog is flipped out of the DNA helix in the same manner as cytosine, 5-methylcytosine, and 5-fluorocytosine. However, no formation of a covalent bond was detected between the sulfur atom of the catalytic site nucleophile, cysteine 81, and the pyrimidine C6 carbon. These results indicate that DZCyt can occupy the active site of M.HhaI as a transition state mimic and, because of the high degree of affinity of its interaction with the enzyme, it can act as a potent inhibitor of methylation.

Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base.

Three structures have been determined for complexes between HhaI methyltransferase (M.HhaI) and oligonucleotides containing a G:A, G:U or G:AP (AP = abasic or apurinic/apyrimidinic) mismatch at the target base pair. The mismatched adenine, uracil and abasic site are all flipped out of the DNA helix and located in the enzyme's active-site pocket, adopting the same conformation as in the flipped-out normal substrate. These results, particularly the flipped-out abasic deoxyribose sugar, provide insight into the mechanism of base flipping. If the process involves the protein pushing the base out of the helix, then the push must take place not on the base, but rather on the sugar-phosphate backbone. Thus rotation of the DNA backbone is probably the key to base flipping.

Characterization of the Ras binding domain of the RalGDS-related protein, RLF.

The Ras binding domain (RBD) of Rlf, a member of the RalGDS family of proteins, was characterized. Using an ELISA-based technique, the relative binding affinity of Rlf for a variety of mutant Ras proteins was determined. Rlf had significantly different binding characteristics than the Raf-1 RBD. The minimal effective Ras binding domain was defined as residues 657-778 using N- and C-terminal deletions of Rlf. Using the PHD algorithm, the secondary structure of this domain was predicted to be similar to the ubiquitin superfold previously identified in the Raf-1 RBD. When the predicted secondary structure of the Rlf-RBD was aligned with the known secondary structure of the Raf-RBD, amino acids in Raf-1 essential for Ras binding were found to also be conserved in Rlf. Consistent with this observation, alanine substitution of one of these residues (K687) in Rlf significantly reduced affinity for Ras-GTP.

Expression, purification, mass spectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific).

The type II DNA-methyltransferase (cytosine N4-specific) M.PvuII was overexpressed in Escherichia coli, starting from the internal translation initiator at Met14. Selenomethionine was efficiently incorporated into this short form of M.PvuII by a strain prototrophic for methionine. Both native and selenomethionyl M.PvuII were purified to apparent homogeneity by a two-column chromatography procedure. The yield of purified protein was approximately 1.8 mg/g bacterial paste. Mass spectrometry analysis of selenomethionyl M.PvuII revealed three major forms that probably differ in the degree of selenomethionine incorporation and the extent of selenomethionine oxidation. Amino acid sequencing and mass spectrometry analysis of selenomethionine-containing peptides suggests that Met30, Met51, and Met261 were only partially replaced by selenomethionine. Furthermore, amino acid 261 may be preferentially oxidized in both native and selenomethionyl form. Selenomethionyl and native M.PvuII were crystallized separately as binary complexes of the methyl donor S-adenosyl-L-methionine in the monoclinic space group P2(1). Two complexes were present per asymmetric unit. Six out of nine selenium positions (per molecule), including the three that were found to be partially substituted, were identified crystallographically.

Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.

We have determined the structure of Pvu II methyltransferase (M. Pvu II) complexed with S -adenosyl-L-methionine (AdoMet) by multiwavelength anomalous diffraction, using a crystal of the selenomethionine-substituted protein. M. Pvu II catalyzes transfer of the methyl group from AdoMet to the exocyclic amino (N4) nitrogen of the central cytosine in its recognition sequence 5'-CAGCTG-3'. The protein is dominated by an open alpha/beta-sheet structure with a prominent V-shaped cleft: AdoMet and catalytic amino acids are located at the bottom of this cleft. The size and the basic nature of the cleft are consistent with duplex DNA binding. The target (methylatable) cytosine, if flipped out of the double helical DNA as seen for DNA methyltransferases that generate 5-methylcytosine, would fit into the concave active site next to the AdoMet. This M. Pvu IIalpha/beta-sheet structure is very similar to those of M. Hha I (a cytosine C5 methyltransferase) and M. Taq I (an adenine N6 methyltransferase), consistent with a model predicting that DNA methyltransferases share a common structural fold while having the major functional regions permuted into three distinct linear orders. The main feature of the common fold is a seven-stranded beta-sheet (6 7 5 4 1 2 3) formed by five parallel beta-strands and an antiparallel beta-hairpin. The beta-sheet is flanked by six parallel alpha-helices, three on each side. The AdoMet binding site is located at the C-terminal ends of strands beta1 and beta2 and the active site is at the C-terminal ends of strands beta4 and beta5 and the N-terminal end of strand beta7. The AdoMet-protein interactions are almost identical among M. Pvu II, M. Hha I and M. Taq I, as well as in an RNA methyltransferase and at least one small molecule methyltransferase. The structural similarity among the active sites of M. Pvu II, M. Taq I and M. Hha I reveals that catalytic amino acids essential for cytosine N4 and adenine N6 methylation coincide spatially with those for cytosine C5 methylation, suggesting a mechanism for amino methylation.

IMP dehydrogenase from Pneumocystis carinii as a potential drug target.

Mycophenolic acid, a specific inhibitor of IMP dehydrogenase (IMPDH; EC 1.1.1.205), is a potent inhibitor of Pneumocystis carinii growth in culture, suggesting that IMPDH may be a sensitive target for chemotherapy in this organism. The IMPDH gene was cloned as a first step to characterizing the enzyme and developing selective inhibitors. A 1.3-kb fragment containing a portion of the P. carinii IMPDH gene was amplified by PCR with two degenerate oligonucleotides based on conserved sequences in IMPDH from humans and four different microorganisms. Northern hybridization analysis showed the P. carinii IMPDH mRNA to be approximately 1.6 kb. The entire cDNA encoding P. carinii IMPDH was isolated and cloned. The deduced amino acid sequence of P. carinii IMPDH shared homology with bacterial (31 to 38%), protozoal (48 to 59%), mammalian (60 to 62%), and fungal (62%) IMPDH enzymes. The IMPDH cDNA was expressed by using a T7 expression system in an IMPDH-deficient strain of Escherichia coli (strain S phi 1101). E. coli S phi 1101 cells containing the P. carinii IMPDH gene were able to grow on medium lacking guanine, implying that the protein expressed in vivo was functional. Extracts of these E. coli cells contained IMPDH activity that had an apparent Km for IMP of 21.7 +/- 0.3 microM and an apparent Km for NAD of 314 +/- 84 microM (mean +/- standard error of the mean; n = 3), and the activity was inhibited by mycophenolic acid (50% inhibitory concentration, 24 microM; n = 2).

A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase.

The crystal structure of HhaI methyltransferase complexed with non-palindromic duplex DNA, containing a hemimethylated recognition sequence, and with the cofactor analog S-adenosyl-L-homocysteine (AdoHcy), has been determined. The structure provides an explanation for the stronger affinities of DNA methyltransferases for hemimethylated DNA than for unmethylated or fully methylated DNA in the presence of AdoHcy. The unmethylated target 2'-deoxycytidine flips out of the DNA helix and the CH group at position 5 makes van der Waals' contacts with the sulfur atom of AdoHcy. Selectivity/preference for hemimethylated over fully methylated DNA may thus reflect interactions among the chemical substituent (H or CH3) at the C5 position of the flipped cytosine, protein and the bound AdoHcy. The 5-methyl-2'-deoxycytidine on the complementary strand remains in the DNA helix, with the methyl group almost perpendicular to the carboxylate group of Glu239, which is part of the sequence recognition loop. Thus, selectivity/preference for hemimethylated over unmethylated DNA appears to result largely from van der Waals' contacts between the planar Glu239 carboxylate and the methyl group of the 5-methyl-2'-deoxycytidine. Furthermore, the positive electrostatic potential originating from the bound AdoHcy extends to the DNA phosphate groups flanking the flipped cytosine. The increased binding to DNA by long-range electrostatic interactions should also occur with the methyl donor S-adenosyl-L-methionine.

Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes.

The refined crystal structures of HhaI methyltransferase complexed with cognate unmethylated or methylated DNA together with S-adenosyl-L-homocysteine, along with the previously-solved binary and covalent ternary structures, offer a detailed picture of the active site at individual stages throughout the reaction cycle. This picture supports and extends a proposed mechanism for C5-cytosine methylation that may be general for the whole family of C5-cytosine methyltransferases. The structures of the two new complexes have been refined to crystallographic R-factors of 0.189 and 0.178, respectively, at 2.7 A resolution. We observe that both unmethylated 2'-deoxycytidine and 5-methyl-2'-deoxycytidine flip out of the DNA helix and fit into the active site of the enzyme. The catalytic sulfur atom of Cys81 interacts strongly with C6. The C5 methyl group of the flipped 5-methyl-2'-deoxycytidine is bent approximately 50 degrees out of the plane of the cytosine ring and towards the sulfur atom of S-adenosyl-L-homocysteine. This unusual position is probably due to partial sp3 character at C5 and C6 and to steric effects of the conserved amino acid residues Pro80 and Cys81. Two water molecules are held near the hydrophobic edge (C5 and C6) of the flipped cytosine by two conserved amino acid residues (Gln82 and Asn304) and the phosphoryl oxygen atom of the phosphate group 3' to the flipped nucleotide, and one of them may serve as the general base for eliminating the proton from C5. Protonation of the cytosine N3 during the methylation reaction may involve Glu119, which itself might be protonated via a water-mediated interaction between the terminal carboxyl group of Glu119 and the amino group of the methionine moiety of S-adenosyl-L-methionine. The cofactor thus plays two key roles in the reaction.

Structure-based sequence alignment of three AdoMet-dependent DNA methyltransferases.

M.HhaI, M.TaqI and COMT are DNA methyltransferases (MTases) which catalyze the transfer of a methyl group from the cofactor AdoMet to C5 of cytosine, to N6 of adenine and to a hydroxyl group of catechol, respectively. The larger catalytic domains of the bilobal proteins, M.HhaI and M.TaqI, and the entire single domain of COMT have an alpha/beta structure containing a mixed central beta-sheet. These domains have very similar folding. By allowing appropriate 'insertions' or 'deletions' in the backbones of the three structures, it was possible to find more conserved motifs in M.TaqI and COMT. The similarity in protein folding and the equivalence of amino-acid sequences revealed by the structural alignment indicate that many AdoMet-dependent MTases may share a common catalytic domain structure.

Universal catalytic domain structure of AdoMet-dependent methyltransferases.

The DNA methyltransferases, M.HhaI and M.TaqI, and catechol O-methyl-transferase (COMT) catalyze the transfer of a methyl group from the cofactor S-adenosyl-L-methionine (AdoMet) to carbon-5 of cytosine, to nitrogen-6 of adenine, and to a hydroxyl group of catechol, respectively. The catalytic domains of the bilobal proteins, M.HhaI and M.TaqI, and the entire single domain of COMT have similar folding with an alpha/beta structure containing a mixed central beta-sheet. The functional residues are located in equivalent regions at the carboxyl ends of the parallel beta-strands. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-dependent methyltransferases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-dependent methyltransferases from their amino acid sequences.

Phonetic features by babies with unilateral cleft lip and palate.

Twenty-three babies with nonsyndromic unilateral cleft lip and palate were audiotaped at regular intervals from 5 to 35 months of age. Narrow phonetic transcription of their comfort-state vocalizations and word approximations was accomplished to describe phonetic development over time and according to the nonrandomized age of palatoplasty. The babies that had earlier palatal repair produced significantly higher percentages of oral stops after 12 months of age than babies with similar clefts that had later palatal repair. No significant differences are evident, however, according to age of palatoplasty, for mean frequency use of oral fricatives up to 3 years of age. For all 23 babies, regardless of the age of palatoplasty intervention, time is an even stronger variable than age of palatoplasty for development of palatal, alveolar and velar place features, oral stops, and oral fricatives.

Identification of children with and without cleft palate from tape-recorded samples of early vocalizations and speech.

Thirty judges (5 speech pathologists, 10 mothers of children with cleft palate, and 15 mothers of noncleft children) listened to 90 tape-recorded samples of early vocalizations/speech obtained from noncleft babies and babies with cleft palate. Each sample was classified by the judges as normal or abnormal. As a group, the speech pathologists classified only 60% of the cleft samples as abnormal and 59% of the normal samples as normal. The cleft and noncleft mother groups, on the other hand, classified 37% and 25% of the cleft samples as abnormal and 59% and 73% of the normal samples as normal. Poor interjudge agreement was evident within and across the three groups of judges. The poor reliability demonstrated by the speech pathologists in identifying babies with unrepaired clefts appeared related more to a difference in interpretation of the perceptual data than an inability to hear salient information.

Phonetic analyses of the speech development of babies with cleft palate.

Phonetic transcription was completed of the vocalizations of 23 babies with cleft palate at 9 specified ages from 3 to 36 months of age. Frequency of occurrence was calculated for: (1) consonant place features, (2) consonant manner features, (3) stop types, (4) fricative types, (5) vowel place features, and (6) vowel height features. The data are discussed for the entire population, for those babies with greater palatal tissue for whom palatoplasty was conducted at or prior to 12 months of age and for those babies with lesser tissue for whom palatoplasty was conducted after 12 months of age. Results suggest that (1) neither group used oral place features at the rate produced by babies born with intact velopharyngeal mechanisms, but that (2) the greater tissue group exhibited somewhat higher emergence of oral stop and fricative productions.