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PubMed1993

Thoracic outlet syndrome--a myofascial variant: Part 3. Structural and postural considerations.

Thoracic outlet syndrome involves more than just local neurovascular compression. Myofascial release treatments and stretching exercises may be only partially or temporarily successful unless all related components of somatic dysfunction, including craniosacral mechanisms, are addressed. Structural and postural abnormalities in the frontal plane, as with a short leg, and in the sagittal plane, such as lumbopelvic imbalances, as well as neural involvement all contribute to thoracic outlet syndrome symptoms. Once segmental restrictions are treated and symptoms diminish, postural correction and strengthening exercises may be initiated. Osteopathic diagnosis and treatment of the local, regional, and remote structural problems is necessary for optimal treatment of thoracic outlet syndrome and the maintenance of a symptom-free status.

Humans↗
PubMed1995

Intact protein electrospray ionization tandem mass spectrometry can be the sole technique used for confirming the structure of a variant hemoglobin.

A mutation within the human alpha-globin resulting in an 18 u mass increment was characterized by sequencing the intact M(r) 15000 protein in the gas phase by electrospray ionization tandem mass spectrometry. No separation of the variant protein from its normal counterpart and other components of the hemolysate was performed prior to mass spectrometric analysis. Collision-induced dissociation of the globin molecules carrying 18 protons was affected by their exposure to methane in the collision cell of a triple quadrupole mass spectrometer equipped with an electrospray ion source. Consideration of the major fragmentation ions (b758+, y"284+ and y"617+) narrowed down the mutation site to the last 28 amino acid residues within the protein sequence. Examination of low-abundance product ions allowed the unequivocal identification of the mutation as alpha 136 Leu --> Met, a hemoglobin previously named Hb Chicago.

Amino Acid Sequence↗
PubMed1999

X-ray structure of the Asn276Asp variant of the Escherichia coli TEM-1 beta-lactamase: direct observation of electrostatic modulation in resistance to inactivation by clavulanic acid.

The clinical use of beta-lactam antibiotics combined with beta-lactamase inactivators, such as clavulanate, has resulted in selection of beta-lactamases that are insensitive to inactivation by these molecules. Therefore, therapeutic combinations of an enzyme inactivator and a penicillin are harmless for bacteria harboring such an enzyme. The TEM beta-lactamase variants are the most frequently encountered enzymes of this type, and presently, 20 variants are designated as inhibitor-resistant TEM ("IRT") enzymes. Three mutations appear to account for the phenotype of the majority of IRT enzymes, one of them being the Asn276Asp substitution. In this study, we have characterized the kinetic properties of the inhibition process of the wild-type TEM-1 beta-lactamase and of its Asn276Asp variant with the three clinically used inactivators, clavulanic acid (clavulanate), sulbactam, and tazobactam, and we report the X-ray structure for the mutant variant at 2.3 A resolution. The changes in kinetic parameters for the interactions of the inhibitors with the wild-type and the mutant enzymes were more pronounced for clavulanate, and relatively inconsequential for sulbactam and tazobactam. The structure of the Asn276Asp mutant enzyme revealed a significant movement of Asp276 and the formation of a salt bridge of its side chain with the guanidinium group of Arg244, the counterion of the inhibitor carboxylate. A water molecule critical for the inactivation chemistry by clavulanate, which is observed in the wild-type enzyme structure, is not present in the crystal structure of the mutant variant. Such structural changes favor the turnover process over the inactivation chemistry for clavulanate, with profound phenotypic consequences. The report herein represents the best studied example of inhibitor-resistant beta-lactamases.

Asparagine↗
PubMed1986

Polymorphism of the human complement C4 and steroid 21-hydroxylase genes. Restriction fragment length polymorphisms revealing structural deletions, homoduplications, and size variants.

Several autoimmune disorders as well as congenital adrenal hyperplasia (CAH) are either associated or closely linked with genetic variants of the fourth component of complement (C4A and C4B) and the enzyme steroid 21-hydroxylase (21-OH). These proteins are encoded by genes that are located downstream from the genes for complement proteins, C2 and factor B (BF) between HLA-B and -DR in the major histocompatibility complex (MHC). Previous studies of variants and null alleles were based on electrophoretic mobility of C4 protein and linkage with disease phenotypes. These data did not permit analysis of the basis for the observed null alleles and duplicated variants. We studied this region of the MHC in 126 haplotypes for a structural analysis of the four adjacent loci, C4A, 21-OHA, C4B, and 21-OHB. About half of the C4 genes typed as C4 null are deleted and several unrecognized homoduplicated C4 alleles were detected. Hence the frequencies of different C4 structural variants must be recalculated based on a direct analysis of the genes. Analysis of the C4/21-OH genes of patients with the classical (salt-wasting) form of CAH showed that some involve a deletion of the C4B and 21-OHB genes; whereas for two only the 21-OHB gene is deleted, i.e., the C4B gene is present. Together, these data provide a better understanding of the mechanisms generating and importance of deleted C4 and 21-OH null alleles in human disease.

Adrenal Hyperplasia, Congenital↗
PubMed2004

The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants.

Missense mutation leading to single amino acid polymorphism (SAP) is the type of mutation most frequently related to human diseases. The Swiss-Prot protein knowledgebase records information on such mutations in various sections of a protein entry, namely in the "feature," "comment," and "reference" fields. To facilitate users in obtaining the most relevant information about each human SAP recorded in the knowledgebase, the Swiss-Prot Variant web pages were created to provide a summary of available sequence information, as well as additional structural information on each variant. In particular, the ModSNP database was set up to store information related to SAPs and to manage the modeling of SAPs onto protein structures via an automatic homology modeling pipeline. Currently, among the 16,566 human SAPs recorded in the Swiss-Prot knowledgebase (release 42.5, 21 November 2003), more than 25% have corresponding 3D-models. Of these variants, 47% are related to disease, 26% are polymorphisms, and 27% are not yet clearly classified. The ModSNP database is updated and the subsequent model construction pipeline is launched with each weekly Swiss-Prot release. Thus, the ModSNP database represents a valuable resource for the structural analysis of protein variation. The Swiss-Prot variant pages are accessible from the NiceProt view of a Swiss-Prot entry on the ExPASy server (www.expasy.org/), via a hyperlink created for the stable and unique identifier FTId of each human SAP.

Amino Acid Substitution↗
PubMed2001

Crystal structures of bovine beta-lactoglobulin in the orthorhombic space group C222(1). Structural differences between genetic variants A and B and features of the Tanford transition.

The crystal structures of beta-lactoglobulin genetic variants A and B have been determined in the orthorhombic space group C222(1) (lattice Y) by X-ray diffraction at 2.0 A and 1.95 A resolution, respectively. The structural comparison shows that both variants exhibit the open conformation of the EF loop at the pH of crystallization (pH 7.9), in contrast to what has been reported for the same genetic variants at pH 7.1 in the trigonal space group P3221 (lattice Z) [Qin, B.Y., Bewley, M.C., Creamer, L.K., Baker, E.N. & Jameson, G.B. (1999) Protein Sci. 8, 75-83]. Furthermore, it was found that the stereochemical environment of Tyr42 changes significantly with pH variation between pH 7 and pH 8. This may provide a structural explanation for an as yet unexplained feature of the Tanford transition, namely the increase in exposure of a tyrosine residue.

Animals↗
PubMed1997

Developmentally regulated alternative splicing of mRNAs encoding N-terminal tau variants in the rat hippocampus: structural and functional implications.

Tau protein variants are axonal microtubule-associated phosphoproteins whose expression correlates with developmentally regulated neurite outgrowth. A single gene encodes multiple tau transcripts via complex alternative splicing. We studied the expression of the mRNAs encoding N-terminal variants of tau, and we showed distinct alternative splicing of exons 2 and 3 in nervous tissues of the adult rat, including the inner ear, hippocampus, cortex, striatum, brainstem, cerebellum, olfactory bulb and retina. Using the reverse transcriptase-coupled polymerase chain reaction and in situ hybridization, we then focused our developmental study on hippocampal neurons, both in vivo and in vitro, to address the developmental and spatial expression of the alternatively spliced mRNAs encoding N-terminal variants of tau. Tau mRNAs devoid of exons 2 and 3 were present throughout development, although their levels decreased in adults. Those containing exon 2 but not exon 3 were already present in the hippocampus of newborn rats and their levels increased during the first postnatal week, mainly in the pyramidal cell layer. Tau RNAs containing exons 2 and 3 appeared at the end of this period in the pyramidal cell layer and in the dentate granule cells. Exon 2-containing mRNAs seemed to be associated with cells undergoing axonal sprouting, while exon 3-containing RNAs were expressed in mature neurons that had established their connections. The timing and pattern of tau alternative splicing were maintained in cultured hippocampal neurons, suggesting that splicing processes are independent of the organized connectivity and of the environmental cues provided in vivo. Secondary structure predictions of tau variants revealed that the insertion of the exon 3-encoded domain substantially modifies the secondary structure of the N-terminal region of tau. This N-terminal heterogeneity may confer distinct regulatory roles on the tau variants during ontogeny and may contribute to plasticity in the adult rat brain.

Alternative Splicing↗
PubMed2026

Mapping Focal and Generalized Effects of Common Genetic Variants on Human Brain Structure.

Genome-wide association studies (GWAS) have advanced the quest to understand how specific genetic variants influence human brain structure and function. Recent work has identified hundreds of common variants associated with subcortical brain volumes, sparking interest in how these genetic markers overlap across brain networks. While this can be estimated by hierarchical clustering of the genetic correlation matrix to identify modular patterns of shared architecture, no brain-wide maps of these effects are available. To address this, we computed polygenic scores (PGS) from loci associated with ten brain volume regions of interest (ROIs): nine major subcortical structures and intracranial volume, with each locus weighted by its association with regional volume. In an independent sample from the discovery GWAS, we performed large-scale segmentation of 3D volumetric T1-weighted MRI scans using voxel-based morphometry (VBM) to map 3D profile of regions where gray matter volume (GMV) was associated with each PGS. We found statistically significant, localized effects for PGS defined for the amygdala, thalamus, and basal ganglia, but PGS for brainstem volume was associated with widespread differences throughout the brain. These brain-wide maps reveal patterns consistent with both localized and distributed genetic influences, offering a novel approach to interpret the genomic architecture of brain structure.

GWAS↗
PubMed2001

Recurrent miscarriage and variant alleles of mannose binding lectin, tumour necrosis factor and lymphotoxin alpha genes.

Variant alleles of the mannose binding lectin (MBL) gene are associated with increased susceptibility to infection and polymorphisms of tumour necrosis factor and lymphotoxin alpha genes (TNF, LTA) are associated with increased severity of infection. Studies have associated recurrent miscarriage with low serum mannose binding lectin concentrations and premature membrane rupture and preterm delivery with elevated maternal and fetal levels of TNF and the TNF (- 308) polymorphism. In this study the frequencies of variant MBL, TNF and LTA alleles in 76 Caucasian couples with idiopathic recurrent miscarriage were compared with those in 69 Caucasian control couples with no history of miscarriage and at least one previous live birth. A new assay based on hybridization to immobilized sequence-specific oligonucleotides (SSO) was used to rapidly detect nine MBL, two TNF and two LTA sequence variants. The assay genotyped all the structural and promoter MBL variants known to influence serum MBL concentrations. This assay was more reliable than restriction digestion or nested allele-specific PCR for the structural variants at codon 54 or 52, respectively. Reliability for codon 57 alleles was not assessed because of the low frequency in this population. The MBL haplotype frequencies in antenatal controls were similar to those reported in other control populations. The frequencies of structural variant MBL genes and of low, medium and high MBL level haplotypes were similar in the recurrent miscarriage and control couples. The TNF and LTA haplotype frequencies were similar in the recurrent miscarriage and control couples. In this carefully defined population no association has been found between recurrent miscarriage and variant alleles of the MBL, TNF or LTA genes.

Abortion, Habitual↗
PubMed1988

Hemoglobin Saverne: a new variant with elongated beta chains: structural and functional properties.

A 26-year-old French woman born in Saverne (France) was found to have Heinz body hemolytic anemia. Isoelectrofocusing showed the presence of an abnormal band amounting to 35% of the total hemoglobin concentration, suggesting a beta variant. Structural analysis of the abnormal beta chain showed an elongated C-terminal segment. Histidine 143 is replaced by a proline and the C-terminal sequence is identical to the corresponding segment of Hb Cranston. This new variant, named Hb Saverne, has beta chains composed of 156 amino acid residues. Studies of its functional properties showed that Hb Saverne is an unstable, high affinity variant with low cooperativity.

Adult↗
PubMed1983

Recombination in simian virus 40-infected cells. Structure of naturally arising variants ev-2114, ev-2102, and ev-1110.

The complete nucleotide sequence has been determined for three newly cloned evolutionary variants from two different independently generated evolutionary series (1100 and 2100 series) of simian virus 40 (SV40). These naturally arising variants, designated ev-1110, ev-2102, and ev-2114, were isolated after five high multiplicity serial passages. The structure of the variants consists of a monomeric unit tandemly repeated four times (ev-2102 and ev-2114) or six times (ev-1110) in the variant genome; the variants have four or six copies, respectively, of the viral origin signal for DNA replication. The DNA content in the three variants is vastly different in that the genome of variant ev-2114 contains only rearranged viral sequences, while variant ev-2102 contains a substitution with monkey DNA sequences consisting of a nearly complete dimeric unit of Alu family sequences as well as less repetitive sequences and variant ev-1110 contains monkey DNA sequences derived solely from repetitive alpha-component DNA. Recombination events, cellular sequences, and structural features of these and other naturally arising SV40 variants are compared.

Base Sequence↗
PubMed2006

Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate.

Human immunodeficiency virus type 1 (HIV-1) protease processes and cleaves the Gag and Gag-Pol polyproteins, allowing viral maturation, and therefore is an important target for antiviral therapy. Ligand binding occurs when the flaps open, allowing access to the active site. This flexibility in flap geometry makes trapping and crystallizing structural intermediates in substrate binding challenging. In this study, we report two crystal structures of two HIV-1 protease variants bound with their corresponding nucleocapsid-p1 variant. One of the flaps in each of these structures exhibits an unusual "intermediate" conformation. Analysis of the flap-intermediate and flap-closed crystal structures reveals that the intermonomer flap movements may be asynchronous and that the flap which wraps over the P3 to P1 (P3-P1) residues of the substrate might close first. This is consistent with our hypothesis that the P3-P1 region is crucial for substrate recognition. The intermediate conformation is conserved in both the wild-type and drug-resistant variants. The structural differences between the variants are evident only when the flaps are closed. Thus, a plausible structural model for the adaptability of HIV-1 protease to recognize substrates in the presence of drug-resistant mutations has been proposed.

Crystallography, X-Ray↗
PubMed2004

The crystal structure of the Y66L variant of green fluorescent protein supports a cyclization-oxidation-dehydration mechanism for chromophore maturation.

The crystal structure of a colorless variant of green fluorescent protein (GFP) containing the Y66L substitution has been determined to 1.5 A. Crystallographic evidence is presented for the formation of a trapped intermediate on the pathway of chromophore maturation, where the peptide backbone of residues 65-67 has condensed to form a five-membered heterocyclic ring. The hydroxyl leaving group remains attached to the ring as confirmed by high-resolution electrospray mass spectrometry. The alpha-carbon of residue 66 exhibits trigonal planar geometry, consistent with ring oxidation by molecular oxygen. Side chain positions of surrounding residues are not perturbed, in contrast to structural results obtained for the GFPsol-S65G/Y66G variant [Barondeau, D. P., Putnam, C. D., Kassmann, C. J., Tainer, J. A., and Getzoff, E. D. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 12111-12116]. The data are in accord with a reaction pathway in which dehydration is the last of three chemical steps in GFP chromophore formation. A novel mechanism for chromophore biosynthesis is proposed: when the protein folds, the backbone condenses to form a cyclopentyl tetrahedral intermediate. In the second step, the ring is oxidized by molecular oxygen. In the third and final step, elimination of the hydroxyl leaving group as water is coupled to a proton transfer reaction that may proceed via hydrogen-bonded solvent molecules. Replacement of the aromatic Tyr66 with an aliphatic residue appears to have a profound effect on the efficiency of ring dehydration. The proposed mechanism has important implications for understanding the factors that limit the maturation rate of GFP.

Amino Acid Substitution↗
PubMed1993

Wild-type p53 differentially affects tumorigenic and metastatic potential of murine metastatic cell variants.

The structure and the function of the p53 gene were studied in two metastatic cell variants derived from Lewis lung carcinoma. Single missense mutation at codon 334 was detected in the p53 gene of both cell variants. In spite of the identical mutation, the in vitro and in vivo growth rates of the two cell variants were differentially affected by the constitutive expression of exogenous wild-type (wt) p53 gene. In fact, only the more malignant cell line (C87) was severely affected by the wt-p53 gene introduction. However, the in vivo effects on this cell line were transient because during serial in vivo passages, cell populations lacking the wt-p53 gene were selected. Genetic mechanisms responsible for the resistance of the less metastatic cell variant (BC215) to the wt-p53 expression, were investigated. Intrinsic ability to mutate exogenous cDNA sequences was tested. We report that BC215 cells continued to express exogenous wt-p53 sequences after several in vitro passages. The expression of mdm2 gene was evaluated. The data demonstrated that BC215 cells constitutively express higher levels of mdm2 gene than C87 cells. We conclude that the overexpression of this gene might be responsible for the resistance of BC215 cells to exogenous wt-p53 gene expression.

Animals↗
PubMed2003

Structural basis of the GM2 gangliosidosis B variant.

To study the structural basis of the GM2 gangliosidosis B variant, we constructed the three-dimensional structures of the human beta-hexosaminidase alpha-subunit and the heterodimer of the alpha- and beta-subunits, Hex A, by homology modeling. The alpha-subunit is composed of two domains, domains I and II. Nine mutant models due to specific missense mutations were constructed as well and compared with the wild type to determine structural defects. These nine mutations were divided into five groups according to structural defects. R178H is deduced to affect the active site directly, because R178 is important for binding to the substrate. C458Y and W420C are predicted to cause drastic structural changes in the barrel structure carrying the active site pocket. R504C/H is deduced to introduce a disruption of an essential binding with D494 in the beta-subunit for dimerization. R499C/H, located in an extra-helix, is deduced to disrupt hydrogen bonds with domain I and the barrel. R170W and L484P are deduced to affect the interface between domains I and II, causing destabilization. The structural defects reflect the biochemical abnormalities of the disease.

Amino Acid Substitution↗
PubMed1982

High density lipoprotein-3 heterogeneity in subjects with the apo-AIMilano variant.

The structure of high density lipoproteins (HDL) isolated from subjects with the AIMilano (AIM) apoprotein variant was studied by the use of the cross-linking reagent dimethylsuberimidate. The HDL2 subfraction is markedly reduced, as compared to control subjects; the HDL3 subfraction, on the other hand, shows a marked heterogeneity, being characterized by at least three particle subpopulations, identified as HDL3-I, HDL3-II, and HDL3-III. The HDL3 fraction purified from the AI Milano subjects eluted as a symmetrical peak from a 6% agarose column, corresponding to a unimodal particle size distribution. The content of the different HDL3 particles, detected by cross-linking, varied widely along the elution profile, the tail of the peak being enriched in anomalous particles of very small size (HDL3-III). Apoprotein compositional studies indicated that these small HDL3-III may be enriched in the AIM monomer, the larger particles containing more AIM-AII complexes and AIM dimers. All the anomalous HDL3 particles are triglyceride enriched, with a decreased cholesterol ester content. They may be an intermediate product in the cholesterol transfer chain between HDL and very low density lipoproteins, or be generated during interconversion of HDL. These particles may have a functional role in tissue cholesterol homeostasis; their unusual compositional changes may help explain the protection of the studied subjects from tissue cholesterol deposition, in spite of the marked decrease of the total HDL fraction.

Amino Acids↗
PubMed2005

Structural differences between allelic variants of the ovine prion protein revealed by molecular dynamics simulations.

We have modeled ovine prion protein (residues 119-233) based on NMR structures of PrP from other mammalian species. Modeling of the C-terminal domain of ovine PrP predicts three helices: helix-1 (residues 147-155), flanked by two short beta-strands; helix-2 (residues 176-197), and helix-3 (residues 203-229). Molecular dynamics simulations on this model of ovine PrP have determined structural differences between allelic variants. At neutral pH, limited root mean-squared (RMS) fluctuations were seen in the region of helix-1; between beta-strand-2 and residue 171, and the loop connecting helix-2 and helix-3. At low pH, these RMS fluctuations increased and showed allelic variation. The extent of RMS fluctuation between beta-strand 2 and residue 171 was ARR > ARQ > VRQ. This order was reversed for the loop region connecting helix-2 and helix-3. Although all three variants have the potential to display an extended helix at the C-terminal region of helix-1, the major influence of the VRQ allele was to restrict the conformations of the Asn162 and Arg139 side-chains. Variations observed in the simulations in the vicinity of helix-1 correlated with reactivity of C-terminal specific anti-PrP monoclonal antibodies with peripheral blood cells from scrapie-susceptible and -resistant genotypes of sheep: cells from VRQ homozygous sheep showed uniform reactivity, while cells from ARQ and ARR homozygous sheep showed variable binding. Our data show that molecular dynamics simulations can be used to determine structural differences between allelic variants of ovine PrP. The binding of anti-PrP monoclonal antibodies to ovine blood cells may validate these structural predictions.

Animals↗