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PubMed1991

Apolipoprotein C-III(Lys58----Glu). Identification of an apolipoprotein C-III variant in a family with hyperalphalipoproteinemia.

Apolipoprotein C-III is a major protein constituent of triglyceride rich lipoproteins and HDL. It occurs in plasma in three isoforms differing by their sialic acid content. Apo C-III putatively inhibits lipolysis and the apo E mediated hepatic uptake of remnants from triglyceride rich particles. We identified a heterozygous carrier of an apolipoprotein C-III variant by the presence of additional bands after isoelectric focusing (IEF) of VLDL. Structural analysis of the variant protein by HPLC, time-of-flight secondary ion mass spectrometry, and automated gas phase sequencing revealed a lysine to glutamic acid replacement in position 58. The underlying A to G exchange was verified by direct sequencing subsequent to amplification by polymerase chain reaction of exon 4 of the apo C-III gene. Family studies revealed vertical transmission of this defect. The two variant carriers exhibited plasma concentrations of HDL cholesterol and apo A-I above the 95th percentiles of sex matched controls whereas the unaffected father and sister showed normal values. The plasma concentrations of apo C-III in the two variant carriers were decreased by 30-40% compared with those of the two unaffected family members and to random controls. Using two-dimensional immunoelectrophoresis as well as IEF and subsequent scanning densitometry, we found that the low serum concentration of apo C-III was a consequence of diminished concentrations of the variant apo C-III isoproteins in both VLDL (15% of normal) and HDL (25% of normal). Apo C-III(Lys58----Glu) heterozygotes possessed unusual HDL as demonstrated by nondenaturing gradient gel electrophoresis. They consisted mainly of HDL2b and contained a proportion of atypically large particles, enriched in apo E, with a Stokes diameter of 13-18 nm and resembling HDLc. In conclusion, heterozygosity for a structural apo C-III variant--apo C-III(Lys58----Glu)--was identified in two hyperalphalipoproteinemic subjects characterized by the presence of low plasma apo C-III concentrations and atypically large HDL.

Adult↗

PubMed1999

Mass spectrometric characterization of Q1, a C(9)H(3)Cl(7)N(2) contaminant in environmental samples

Q1, a heptachloro component of unknown structure and origin, was recently identified as a major organochlorine contaminant in samples from Africa and the Antarctic. Gas chromatography in combination with low resolution mass spectrometry (LRMS) was applied to establish a molecular weight of m/z 384 including seven chlorine atoms. Three possible molecular formulae (C(11)H(7)Cl(7), C(10)H(3)Cl(7)O, and C(9)H(3)Cl(7)N(2)) were proposed which could not be distinguished by LRMS. In this presentation the molecular composition of Q1 was studied using gas chromatography in combination with high resolution electron impact ionization mass spectrometry. With the option of further heteroatoms (P, S, N, O, F, and Br), 17 molecular formulae were obtained for the molecular weight of 384 u. In the selected ion monitoring (SIM) mode, performed with a resolution of 16,000, highest response was found at 383.812 or C(9)H(3)Cl(7)N(2). 11 fragment ions detected in the low resolution full scan mass spectrum of Q1 were also investigated in the high resolution SIM mode. In every case, the nitrogen-variant showed highest abundance while the other 16 structural variants could be definitely excluded. These investigations revealed that the molecular formula of Q1 is C(9)H(3)Cl(7)N(2). No stable component with this molecular formula has ever been reported in the literature, to our knowledge. Copyright 1999 John Wiley & Sons, Ltd.

Journal Article↗

PubMed1994

An 1H NMR determination of the three-dimensional structures of mirror-image forms of a Leu-5 variant of the trypsin inhibitor from Ecballium elaterium (EETI-II).

The 3-dimensional structures of mirror-image forms of a Leu-5 variant of the trypsin inhibitor Ecballium elaterium (EETI-II) have been determined by 1H NMR spectroscopy and simulated annealing calculations incorporating NOE-derived distance constraints. Spectra were assigned using 2-dimensional NMR methods at 400 MHz, and internuclear distances were determined from NOESY experiments. Three-bond spin-spin couplings between C alpha H and amide protons, amide exchange rates, and the temperature dependence of amide chemical shifts were also measured. The structure consists largely of loops and turns, with a short region of beta-sheet. The Leu-5 substitution produces a substantial reduction in affinity for trypsin relative to native EETI-II, which contains an Ile at this position. The global structure of the Leu-5 analogue studied here is similar to that reported for native EETI-II (Heitz A, Chiche L, Le-Nguyen D, Castro B, 1989, Biochemistry 28:2392-2398) and to X-ray and NMR structures of the related proteinase inhibitor CMTI-I (Bode W et al., 1989, FEBS Lett 242:285-292; Holak TA et al., 1989a, J Mol Biol 210:649-654; Holak TA, Gondol D, Otlewski J, Wilusz T, 1989b, J Mol Biol 210:635-648; Holak TA, Habazettl J, Oschkinat H, Otlewski J, 1991, J Am Chem Soc 113:3196-3198). The region near the scissile bond is the most disordered part of the structure, based on geometric superimposition of 40 calculated structures. This disorder most likely reflects additional motion being present in this region relative to the rest of the protein. This motional disorder is increased in the Leu-5 analogue relative to the native form and may be responsible for its reduced trypsin binding. A second form of the protein synthesized with all (D) amino acids was also studied by NMR and found to have a spectrum identical with that of the (L) form. This is consistent with the (D) form being a mirror image of the (L) form and not distinguishable by NMR in an achiral solvent (i.e., H2O). The (D) form has no activity against trypsin, as would be expected for a mirror-image form.

Amino Acid Sequence↗

PubMed2025

Defining and cataloging variants in pangenome graphs.

Structural variation causes some human haplotypes to align poorly with the linear reference genome, leading to 'reference bias'. A pangenome reference graph could ameliorate this bias by relating a sample to multiple reference assemblies. However, this approach requires a new definition of a 'genetic variant.' We introduce a definition of pangenome variants and a method, pantree, to identify them. Our approach involves a pangenome reference tree which includes all nodes (sequences) of the pangenome graph, but only a subset of its edges; non-reference edges are variant edges. Our variants are biallelic and have well-defined positions. Analyzing the Minigraph-Cactus draft human pangenome reference graph, we identified 29.6 million genetic variants. Most variants (99.2%) are small, and most small variants (73.9%) are SNPs. 3.5 million variants (11.7%) have a reference allele which is not on GRCh38; these variants are difficult to detect without a pangenome reference, or with existing pangenome-based approaches. They tend to be embedded within tangled, multiallelic regions. We analyze two medically relevant regions, around the HLA-A and RHD genes, identifying thousands of small variants embedded within several large insertions, deletions, and inversions. We release an open-source software tool together with a VCF variant catalogue.

Journal Article↗

PubMed1995

Characterization of cytochrome c variants with high-resolution FTICR mass spectrometry: correlation of fragmentation and structure.

The dissociation of cytochrome c ions (15+ charge state) generated by electrospray ionization has been studied by Fourier transform ion cyclotron resonance mass spectrometry (FTICR) using a sustained off-resonance irradiation/collision-induced dissociation (SORI-CID) technique. Over 95% of the fragment ions can be accurately assigned (to better than 10 ppm), yielding information on the primary sequences of the various proteins. Up to four stages of mass spectrometry (MS4) have been achieved without the need for quadrupole excitation/collisional cooling of the product ions. The subtle structural differences among the cytochrome c variants (from bovine, tuna, rabbit, and horse) are clearly reflected in their fragmentation patterns: replacing 3 out of 104 residues of the cytochrome c is shown to dramatically change the dissociation pattern. Of particular importance are a variety of results indicating that the dissociation of the cytochrome c's is influenced by higher-order structure and charge location, in addition to the primary structure (i.e., sequence). No fragmentation is observed in the region between residues 10-20 and little dissociation between residues 70-90. This is most likely due to the interactions of the heme group with the polypeptide chain, and such a heme "footprinting" pattern is analogous to the protein conformation in solution. These studies demonstrate that electrospray ionization-FTICR using SORI-CID can be a useful tool to probe not only the small differences in the primary sequences of proteins but also suggest the potential for probing their higher-order structures and yielding information not readily available from H/D exchange or circular dichoism studies.

Amino Acid Sequence↗

PubMed1994

Solution structure of the DNA binding octapeptide repeat of the K10 gene product.

A putative transcription factor, the Drosophila K10 gene product, contains eight repeats of the octapeptide sequence SPNQQQHP or close variants. The solution structure of the K10 repeat was studied by NMR using a peptide composed of two SPNQQQHP units (referred to here as HP2). To overcome problems caused by degeneracy of backbone amide signals of Gln residues, a series of synthetic peptides containing an 15N-labelled main chain amide at different positions in HP2 were synthesized. In aqueous trifluoroethanol solution, HP2 folds into two structural units; the SPNQ part of each unit folds into a turn structure, while the C-terminal part shows some helical characteristics but is less structured. The N-terminal turn is likely to provide a core that produces a more stable helical structure upon binding to DNA and probably 'caps' the segmented helical unit at its N-terminus. This model is supported by a DNA footprinting study which shows that one SPNQQQHP unit spans four base pairs upon binding to A/T-rich sequences of DNA.

Amino Acid Sequence↗

PubMed1984

Hb Cordele alpha(2)47 (CE5)Asp----Ala beta 2. A mildly unstable variant observed in black twins.

Hb Cordele, which has an Asp----Ala substitution at position 47 (CE5) of the alpha chain, was discovered in Black twins living in Cordele, Georgia. The structure of this variant was elucidated through analyses of tryptic peptides of the alpha chain which were isolated by high performance liquid chromatography. At birth, Hb Cordele accounted for about 21-23% of total hemoglobin, and for 30.4% in one of the babies at age 3.5 months. Hb Cordele has a normal oxygen affinity, but is mildly unstable at 60 degrees C. Some of its properties have been compared with those of Hb Kokura (alpha 47 Asp----Gly), Hb Hasharon (alpha 47 Asp----His), and Hb Arya (alpha 47 Asp----Asn). Studies on an adult carrier of Hb Cordele were not possible.

Adult↗

PubMed1994

Genomic structure and cloned cDNAs predict that four variants in the kinase domain of serine/threonine kinase receptors arise by alternative splicing and poly(A) addition.

Heterodimers of types I and II serine/threonine kinase receptor monomers compose the active receptor complex for ligands of the transforming growth factor beta family. Here we show that the genomic organization of coding sequences for the intracellular domain of a widely expressed type I serine/threonine kinase receptor is similar to that of the activin type II receptor gene. The genomic structure and cDNA clones indicate that poly(A) addition to alternative exons at each of three carboxyl-terminal coding exon-intron junctions may be a common feature of both type I and II receptor genes. The predicted products are monomers truncated at kinase subdomains VII, IX, and X which vary in kinase activity and potential serine, threonine, and tyrosine phosphorylation sites. These results suggest that combinations of variants that affect the signal-transducing intracellular kinase domain of both type I and II receptor monomers within the transforming growth factor beta ligand family may add to the heterogeneity of biological effects of individual ligands in the family.

Alternative Splicing↗

PubMed1993

The x-ray crystal structure refinements of normal human transthyretin and the amyloidogenic Val-30-->Met variant to 1.7-A resolution.

The x-ray crystal structures of normal human transthyretin (prealbumin) and the amyloidogenic Val-30-Met variant have been refined at 1.7-A resolution to R-values of 0.168 and 0.179, respectively, for 19,882 and 20,362 reflections (Fobs > 2.0 sigma). Standard deviations for stereochemical parameters are 0.018 and 0.022 A for bond distances, 0.030 and 0.038 A for angle distances, and 0.035 and 0.070 A for planar 1-4 distances. The newly refined normal structure shows improvement over the original structure of Blake and Swan (Blake, C. C. F., and Swan, I. D. A. (1971) J. Mol. Biol. 61, 217-224) in stereochemistry and in the conformation of the loop regions. Residues Arg-103, Thr-123, Asn-124, and Pro-125 have now been resolved, and residues 1-9 and 126-127 have been modeled with the aid of simulated annealing refinement. The functional form of transthyretin is a tetramer, having a cylindrical cavity which will bind thyroxine and an exterior binding site for the complex of retinol with retinol-binding protein. The monomer is a beta barrel flattened to become more like a sandwich with residue 30 in the interior. The methionyl for valyl substitution forces the beta sheets of the monomer as much as 1 A apart, resulting in a distortion of the thyroxine-binding cavity, in agreement with the independent observations that the Met-30 variant has low affinity for thyroxine.

Amino Acid Sequence↗

PubMed1975

[Structure and histochemical characteristics of the mucosa of the Vater's ampulla in man (according to materials of aimed biopsies)].

Examination of 52 aimed duodenal biopsies has revealed that there are several variants of the structure of the Vater's papilla mucous membrane. In a number of cases it is identicalto the mucous membrane of the duodenum. In 20 cases the Vater's papilla was covered with mucoid epithelium which was histochemically similar to the epithelium lining the stomach, bile ducts and the gallbladder. The "intermedial" forms found in these cases appearedto be capable to change into mucoid or edging epithelium. The mucous cells occasionally found in the Vater's papilla epithelium might be a variation of goblet cells. It seems that they are secreting by holocrine type.

Ampulla of Vater↗

PubMed1997

Modified substrate specificity of L-hydroxyisocaproate dehydrogenase derived from structure-based protein engineering.

L-2-Hydroxyisocaproate dehydrogenase (L-HicDH) is characterized by a broad substrate specificity and utilizes a wide range of 2-oxo acids branched at the C4 atom. Modifications have been made to the sequence of the NAD(H)-dependent L-HicDH from Lactobacillus confusus in order to define and alter the region of substrate specificity towards various 2-oxocarbonic acids. All variations were based on a 3D-structure model of the enzyme using the X-ray coordinates of the functionally related L-lactate dehydrogenase (L-LDH) from dogfish as a template. This protein displays only 23% sequence identity to L-HicDH. The active site of L-HicDH was modelled by homology to the L-LDH based on the conservation of catalytically essential residues. Substitutions of the active site residues Gly234, Gly235, Phe236, Leu239 and Thr245 were made in order to identify their unique participation in substrate recognition and orientation. The kinetic properties of the L239A, L239M, L236V and T245A enzyme variants confirmed the structural model of the active site of L-HicDH. The substrates 2-oxocaproate, 2-oxoisocaproate, phenylpyruvate, phenylglyoxylate, keto-tert-leucine and pyruvate were fitted into the active site of the subsequently refined model. In order to design dehydrogenases with an improved substrate specificity towards keto acids branched at C3 or C4, amino acid substitutions at positions Leu239, Phe236 and Thr245 were introduced and resulted in mutant enzymes with completely different substrate specificities. The substitution T245A resulted in a relative shift of substrate specificity for keto-tert-leucine of more than 17000 compared with the 2-oxocaproate (kcat/KM). For the substrates branched at C4 a relative shift of up to 500 was obtained for several enzyme variants. A total of nine mutations were introduced and the kinetic data for the set of six substrates were determined for each of the resulting mutant enzymes. These were compared with those of the wild-type enzyme and rationalized by the active site model of L-HicDH. An analysis of the enzyme variants provided new insight into the residues involved in substrate binding and residues of importance for the differences between LDHs and HicDH. After the protein design project was complete the X-ray structure of the enzyme was solved in our group. A comparison between the model and the experimental 3D structure proved the quality of the model. All the variants were designed, expressed and tested before the 3D structure became available.

Alcohol Oxidoreductases↗

PubMed1986

Complex cis-acting regulators and locus structure of Drosophila tissue-specific ADH variants.

Diverse patterns of tissue-specific expression of alcohol dehydrogenase (ADH) among species of the grimshawi subgroup of Hawaiian picture-winged Drosophila suggests control by complex or multiple, independently acting regulatory elements. These elements act by controlling Adh mRNA accumulation in individual tissue types. Restriction mapping of the Adh loci from these species reveals several insertion/deletion differences, one of which lies just outside the 5' end of the structural sequences and correlates with differences in larval patterns of ADH expression. No tissue-specific rearrangement of Adh sequences was observed.

Alcohol Dehydrogenase↗

PubMed1992

Distinct alpha-subunit structures of human insulin receptor A and B variants determine differences in tyrosine kinase activities.

Human insulin receptor isoforms (HIR-A and -B) differ in their alpha-subunit structures which result from alternatively spliced precursor mRNAs. This structural difference causes distinct binding affinities for insulin. To determine the impact of the structural difference on receptor signaling, we characterized the tyrosine kinase activity of HIR-A and HIR-B in vitro and determined the insulin stimulated beta-subunit phosphorylation and tyrosine kinase activation in the intact cell. When 32P incorporation in beta-subunits of equal amounts of isolated HIR-A and HIR-B was measured, an increased 32P incorporation in tyrosine residues of the beta-subunit of HIR-B (2.5-fold) compared to that of HIR-A was found after in vitro insulin stimulation. This was paralleled by an increased rate of phosphorylation (2.0-fold) or poly(GluNa,Tyr 4:1). In vitro analysis of Km values for ATP were similar for HIR-A (Km = 14.3 microM +/- 3.8) and HIR-B (Km = 20.2 microM +/- 8.6), whereas the Vmax of HIR-B was significantly increased (HIR-A Vmax = 5.5 mumol/60 min micrograms-1 +/- 1.4, HIR-B Vmax = 42.5 mumol/60 min micrograms-1 +/- 19.2). HPLC analysis of tryptic beta-subunit phosphopeptides revealed identical patterns, suggesting that the difference in kinase activities is not due to an alteration of the phosphorylation-activation cascade within the beta-subunit. However, when cleavage of the alpha-subunit by short-time trypsinization was used to activate the tyrosine kinase, the differences in 32P incorporation between HIR-A and HIR-B were abolished.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1999

Structural variability of CD44v molecules and reliability of immunodetection of CD44 isoforms using mAbs specific for CD44 variant exon products.

CD44 can be considered structurally and functionally one of the most variable surface molecules. Alternative splicing of variant exons as well as posttranslational modifications of the molecule (differences in glycosylation) generate a rich repertoire of CD44 isoforms (CD44v), some of which seem to play a key role in tumor growth and progression. Immunodetection of CD44 isoforms in vivo, using mAbs specific for CD44 variant exon products, is largely used to identify those CD44 molecules involved in tumor growth and progression and to interfere with CD44-mediated processes. In the present work we demonstrate that the immunoreactivity of some mAbs directed to CD44 exon-specific epitopes can be impaired by the structural variability of the molecule. Our findings demonstrate that (1) specific exon assortment and/or posttranslational modifications of CD44v molecules can mask CD44 exon-specific epitopes; (2) glycosaminoglycan side chains, carried by some CD44v isoforms of high molecular weight, may play a critical role in determining the exact conformation of the molecule, which is necessary for the detection of CD44 variant epitopes by specific mAbs; and (3) in a panel of stable transfectants expressing CD44 N-glycosylation site-specific mutants, generated in the constant region of CD44 extracellular domain, asparagine-isoleucine substitution is sufficient per se to impair the immunoreactivity of several mAbs to pan-CD44. Thus, conformational changes due to the alternative splicing of CD44 variant exons and/or posttranslational modifications of the molecule (different degree of glycosylation), which are cell type-specific, are likely to generate CD44 variants that elude immunodetection. These findings strongly suggest that immunohistochemical analysis of CD44 expression in vitro and in vivo, using mAbs specific for CD44 variant exon epitopes, can potentially be impaired by a large number of false negative results.

Antibodies, Monoclonal↗

PubMed2005

Histone variants: deviants?

Histones are a major component of chromatin, the protein-DNA complex fundamental to genome packaging, function, and regulation. A fraction of histones are nonallelic variants that have specific expression, localization, and species-distribution patterns. Here we discuss recent progress in understanding how histone variants lead to changes in chromatin structure and dynamics to carry out specific functions. In addition, we review histone variant assembly into chromatin, the structure of the variant chromatin, and post-translational modifications that occur on the variants.

Animals↗

PubMed2000

The prion protein globular domain and disease-related mutants studied by molecular dynamics simulations.

In humans, familial forms of transmissible spongiform encephalopathies (TSE; "prion diseases") have been shown to segregate with the exchange of individual amino acids in the prion protein (PrP) sequence. We used the NMR structure of the globular domain of mouse PrP in the cellular form (PrP(C)) as a starting point for investigations by long-time molecular dynamics (MD) simulations at ambient temperature of likely impacts of such mutations on the PrP(C) structure, making use of the fact that species-related amino acid replacements between mouse PrP and human PrP are spatially well separated from the disease-related mutations in human PrP. In the MD simulations these amino acid substitutions were found to have a variety of different effects on the protein structure, with some species showing altered packing of regular secondary structure elements, while other mutants showed no or only strictly localized changes of the structure near the variant amino acid. The fact that some of the disease-related amino acid exchanges cause no measurable change of the PrP(C) structure indicates that their influence on the conformational transition to the scrapie form of PrP may be due to modified intermolecular interactions during the aggregation process.

Amino Acid Substitution↗

PubMed1979

[Solid dendritic angiosarcomas (of the hemangioendothelioma and hemangiopericytoma types in the differential diagnosis of malignant lymphomas)].

A group of 11 cases was used for the closer follow-up of an extraskeletal tumour lik Ewing's sarcoma (9). While mostly soft tissues were affected, its localization was variegated. Throughout the long-term follow-up period there was only one case of non-relapse after extirpation. Most of the tumours became generalized within three years. One exceptional case involved generalization after 13 years. The tumour reveals a mostly solid, seemingly organoid pattern, always, however, with reticular foci or sinusoid in nature. The cells, round or dendritic in appearance, have numerous intercellular connections with Weibel Palade granules occasionally demonstrable in their cytoplasm. In foci of peritheliomatous appearance, such as may exceptionally predominate in the tumour, the tumour cells become elongated, contain an abundance of endoplasmic reticulum, and make up a system of integrated basal membranes. According to its structural and cytological properties, the tumour has the nature of angiosarcoma, mostly of the endothelial type, frequently assuming the nature of the pericytic variant. These transitional structural properties just as the tumour' biological behaviour are unlike Ewing's sarcoma and, for that reason, a change of the name is proposed.

Adolescent↗

PubMed2001

Universal similarity measure for comparing protein structures.

We introduce a new variant of the root mean square distance (RMSD) for comparing protein structures whose range of values is independent of protein size. This new dimensionless measure (relative RMSD, or RRMSD) is zero between identical structures and one between structures that are as globally dissimilar as an average pair of random polypeptides of respective sizes. The RRMSD probability distribution between random polypeptides converges to a universal curve as the chain length increases. The correlation coefficients between aligned random structures are computed as a function of polypeptide size showing two characteristic lengths of 4.7 and 37 residues. These lengths mark the separation between phases of different structural order between native protein fragments. The implications for threading are discussed.

Models, Statistical↗