Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “structural variants”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,009 records · Page 56Linked to original sources
PubMed1995

Structural characterization of two variants of fibulin-1 that differ in nidogen affinity.

Two C-terminal variants C and D of mouse fibulin-1 were purified from the culture medium of stably transfected human kidney cell clones. They showed, after rotary shadowing, a dumbbell-like structure of about 33 nm in length. Pepsin digestion demonstrated stability of the disulfide-bonded domains 1 (anaphylatoxin-like) and II (multiple EGF-like motifs) but not for domain III which is different in the variants. A close similarity of the variants was observed in immunochemical assays indicating that domain III epitopes are not very antigenic. Binding analysis in solid phase assays demonstrated for variant C a 100-fold stronger binding to the basement membrane protein nidogen than for variant D. Both interactions were sensitive to EDTA. Surface plasmon resonance assays confirmed this difference and showed KD = 60 nM for variant C and KD > 1 microM for variant D. Lower binding activities and smaller differences between both variants were observed for the calcium-dependent binding to fibronectin, laminin-1 and collagen IV. Self aggregation into nest-like oligomers was observed at high concentrations of fibulin-1 which was not sensitive to EDTA.

Amino Acid Sequence↗
PubMed1994

Purification of a 24 kD parasitism-specific hemolymph protein from pharate pupae of the Caribbean fruit fly, Anastrepha suspensa.

We report purification of a 24 kD parasitism-specific protein (24 kD PSP) from pharate pupal hemolymph of the Caribbean fruit fly, Anastrepha suspensa, after parasitization by the braconid wasp, Diachasmimorpha (= Biosteres) longicaudata. We previously utilized isoelectric focusing (IEF) and two-dimensional (2-D) gel electrophoresis to demonstrate that the 24 kD PSP consists of two variants with pl 6.7 (more abundant) and pl 6.3. Purification of the more abundant 24 kD PSP variant was accomplished by Concanavalin A (Con A) sepharose B affinity chromatography followed by DEAE column chromatography. A second protocol, utilizing wheat germ agglutinin (WGA) sepharose 6MB affinity chromatography between the ConA and DEAE chromatographic steps, resulted in the purification of a partially deglycosylated form of the 24 kD PSP which retained its immunoreactivity with anti-PSP serum but which exhibited a greater relative migration in sodium dodecyl sulfate (SDS)-PAGE than the pl 6.7 24 kD PSP variant. For structural studies both 24 kD PSP variants were purified from whole hemolymph by flat bed IEF followed by SDS-PAGE. Peptide cleavage profiles in 1-D SDS-PAGE after treatment with BNPS-skatole, CNBr, and endproteinases Lys-C and Asp-N were identical for both 24 kD PSP variants. Primary N-terminus sequences of at least the first 20 amino acid residues of both variants were identical. A secondary sequence of five amino acids residues was detected in both variants at Thr, the seventh amino acid residue from the N-terminus of the primary sequence. These data indicate that both 24 kD PSPs are glycoforms of a branched, apparently homogeneous polypeptide.

Amino Acid Sequence↗
PubMed1998

The minisatellite MSB1, in the fungus Botrytis cinerea, probably mutates by slippage.

A minisatellite was identified in the intron of the ATP synthase of the filamentous fungus Botrytis cinerea, and it was named MSB1. This is the second fungal minisatellite described to date. Its 37-bp repeat unit is AT-rich, and it is found at only one locus in the genome. The introns of 47 isolates of Botrytis species were sequenced. The number of tandem repeats varied only from 5 to 11, but there were many repeat variants. The structure of MSB1 is peculiar: the variants are in the same physical order in all individuals, and this order follows the most parsimonious tree. These original characteristics, together with a total lack of recombination between alleles of the flanking regions, suggest that MSB1 probably mutates by slippage. MSB1 was found in the intron of the ATP synthase of all of the Botrytis species analyzed, but the repeat unit was not found in any other genus examined, including Sclerotinia, which is the genus closest to Botrytis.

Adenosine Triphosphatases↗
PubMed2026

Cytogenetic Diversity of Variant Philadelphia Translocations in Chronic Myeloid Leukemia.

INTRODUCTION: Chronic myeloid leukemia (CML) is a disease characterized by Philadelphia (Ph) translocations. These translocations can be classical or variant. The structural features and diagnostic implications of variant Philadelphia translocations remain incompletely defined, and they display considerable cytogenetic heterogeneity. METHODS: In this retrospective study, variant Ph translocations identified by conventional cytogenetic analysis and fluorescence in situ hybridization (FISH) were systematically classified among 639 patients diagnosed with CML. A total of 35 patients with variant Ph translocations were included in the analysis. Molecular follow-up data, when available, were assessed using RT-qPCR analyses in a subset of patients. RESULTS: Chromosome analysis revealed 2 simple and 33 complex variant Ph translocations. FISH analysis, performed in 20 patients, identified deletions involving BCR, ABL1, or both in a limited number of cases. Additional chromosomal abnormalities and secondary translocations accompanied variant Ph translocations in four patients. The partner chromosomes involved in variant Ph translocations showed marked diversity, involving multiple chromosomal loci. CONCLUSION: Variant Philadelphia chromosome translocations in CML exhibit substantial cytogenetic diversity, reflecting the complexity of their underlying genomic architecture. The rarity and heterogeneity of these rearrangements complicate their classification and interpretation in routine diagnostic practice. Descriptive reporting of variant Ph translocations may contribute to a better understanding of their diagnostic complexity and support more accurate cytogenetic interpretation in CML.

Humans↗
PubMedDate not supplied

[The choice of the type of operation in hydronephrosis in children].

113 hydronephrosis children underwent Andersen-Hynes operation, 62 Calp de Werd operation. The ureteropelvic segment was examined morphologically. 3 macroscopic variants of ureteral structure and 5 variants of leiomyocyte presence in the muscular lining of the ureter are defined. Long-term follow-up results (1-10 years) are available. Resection gave positive results in 80%, graft plastic repair was effective in 92% of cases.

Child↗
PubMed2002

Crystal structure of a staphylokinase: variant a model for reduced antigenicity.

Staphylokinase (SAK) is a 15.5-kDa protein from Staphylococcus aureus that activates plasminogen by forming a 1 : 1 complex with plasmin. Recombinant SAK has been shown in clinical trials to induce fibrin-specific clot lysis in patients with acute myocardial infarction. However, SAK elicits high titers of neutralizing antibodies. Biochemical and protein engineering studies have demonstrated the feasibility of generating SAK variants with reduced antigenicity yet intact thrombolytic potency. Here, we present X-ray crystallographic evidence that the SAK(S41G) mutant may assume a dimeric structure. This dimer model, at 2.3-A resolution, could explain a major antigenic epitope (residues A72-F76 and residues K135-K136) located in the vicinity of the dimer interface as identified by phage-display. These results suggest that SAK antigenicity may be reduced by eliminating dimer formation. We propose several potential mutation sites at the dimer interface that may further reduce the antigenicity of SAK.

Antigens, Bacterial↗
PubMed2000

NMR structures of three single-residue variants of the human prion protein.

The NMR structures of three single-amino acid variants of the C-terminal domain of the human prion protein, hPrP(121-230), are presented. In hPrP(M166V) and hPrP(R220K) the substitution is with the corresponding residue in murine PrP, and in hPrP(S170N) it is with the corresponding Syrian hamster residue. All three substitutions are in the surface region of the structure of the cellular form of PrP (PrP(C)) that is formed by the C-terminal part of helix 3, with residues 218-230, and a loop of residues 166-172. This molecular region shows high species variability and has been implicated in specific interactions with a so far not further characterized "protein X," and it is related to the species barrier for transmission of prion diseases. As expected, the three variant hPrP(121-230) structures have the same global architecture as the previously determined wild-type bovine, human, murine, and Syrian hamster prion proteins, but with the present study two localized "conformational markers" could be related with single amino acid exchanges. These are the length and quality of definition of helix 3, and the NMR-observability of the residues in the loop 166-172. Poor definition of the C-terminal part of helix 3 is characteristic for murine PrP and has now been observed also for hPrP(R220K), and NMR observation of the complete loop 166-172 has so far been unique for Syrian hamster PrP and is now also documented for hPrP(S170N).

Amino Acid Sequence↗
PubMed2007

Identification and computationally-based structural interpretation of naturally occurring variants of human protein C.

Protein C (PC) is a key regulator of blood clotting and inflammation. Its inherited deficiency is associated with venous thromboembolism, and recombinant activated PC is currently used to increase survival in severe sepsis. The molecular basis of inherited PC deficiency is heterogeneous. Due to its multiple physiologic interactions and functions, and its modular structure, natural variants aid in the understanding of the relationship between critical residues and discrete functions. This knowledge has important therapeutic implications in the planning of a recombinant activated PC with a specific therapeutic target and devoid of major collateral effects. A way of predicting important functional consequences of residue variation is the use of molecular modeling and structural interpretation of amino acidic substitutions. A study of 21 out of 32 identified PC gene (PROC) variants is presented. For three of them, localized in the active site, electrostatic potential variation was calculated. For more than half of the studied variants, an explanation for the functional impairment could be derived from computational analysis, allowing a focused choice of which variants it is worthwhile pursuing.

Adolescent↗
PubMed1987

Trypanosoma congolense: structure and molecular organization of the surface glycoproteins of two early bloodstream variants.

The complete primary structures of two variant specific glycoproteins (VSGs) of the nannomonad Trypanosoma (N.) congolense are presented. These coat proteins subserve the function of antigenic variation. The secondary structure potentials of both VSGs have been calculated. The amino acid sequences and secondary structure potentials of these VSGs have been compared with the primary structures and secondary structure potentials of several Trypanosoma brucei complex VSGs. In homologous regions, the T. brucei complex VSGs show a pattern of sharply contrasting secondary structure potentials. It has been suggested previously that this pattern gives rise to different folding structures in different members of this polygene protein family. Thus, different short regions of the polypeptide sequence are exposed as antigenic "caps" on the solvent-exposed surface of intact trypanosomes. A sharply contrasting secondary structure potential pattern is also found in regions of the two T. congolense VSGs. However, there is little homology of primary structure between each of the two T. congolense VSGs and any member of the T. brucei complex VSG polygene family whose primary structure has been determined.

Amino Acid Sequence↗
PubMed2000

Receptor-binding conformation of the "ELR" motif of IL-8: X-ray structure of the L5C/H33C variant at 2.35 A resolution.

The "ELR" (Glu-Leu-Arg) tripeptide sequence near the N-terminus of interleukin-8 (IL-8) contributes a large part of the receptor binding free energy. Prior X-ray and nuclear magnetic resonance (NMR) structures of IL-8 have shown this region of the molecule to be highly mobile. We reasoned that a hydrophobic interaction between the leucine and the neighboring beta-turn might exist in the receptor binding conformation of the N-terminus. To test this hypothesis, we mutated two residues to cysteine and connected the N-terminus to the beta-turn. The mutant retains receptor binding affinity reasonably close to wild type and allows the characterization of a high-affinity conformation that may be useful in the design of small IL-8 mimics. The L5C/H33C mutant is refined to R-values of R = 20.6% and Rfree = 27.7% at 2.35 A resolution. Other receptor binding determinants reside in the "N-loop" found after "ELR" and preceding the first beta-strand. All available structures of IL-8 have been found with one of two distinct N-loop conformations. One of these is relevant for receptor binding, based on NMR results with receptor peptides. The other conformation obscures the receptor-peptide binding surface and may have an undetermined but necessarily different function.

Amino Acid Motifs↗
PubMed1997

Thyroxine binding to transthyretin Met 119. Comparative studies of different heterozygotic carriers and structural analysis.

The majority of the known transthyretin (TTR) variants are associated with amyloidosis, but there are also variants associated with euthyroid hyperthyroxinemia and others are apparently nonpathogenic. TTR Met 119 is a nonpathogenic variant found to be frequent in the Portuguese population. Previous studies on thyroxine (T4) binding to semi-purified TTR from heterozygotic carriers of TTR Met 119, reported by us and other groups, revealed different results. Therefore, to further characterize T4 binding to TTR Met 119 we performed T4-TTR binding studies in homotetrameric-recombinant TTR Met 119 variant and normal TTR. We also studied T4 binding to TTR purified from serum of different heterozygotic carriers of TTR Met 119 including compound heterozygotic individuals carriers of a TTR mutation in the other allele. We observed an increased T4 binding affinity to TTR Met 119 from heterozygotic individuals and compound heterozygotes and this effect of increasing T4 binding affinity was consistent and independent from the mutation present in the other allele. Recombinant homotetrameric TTR Met 119 and heterotetrameric protein from heterozygotic carriers of TTR Met 119 presented similar T4 binding affinity demonstrating the increased T4 binding affinity of TTR Met 119. X-ray crystallography studies performed on the recombinant TTR Met 119 variant revealed structural alterations mainly at the level of residue Leu 110 allowing a closer contact between the hormone and the mutant protein. These results are consistent with the observed T4 binding results.

Binding, Competitive↗
PubMed1992

Three-dimensional structure of a recombinant variant of human pancreatic secretory trypsin inhibitor (Kazal type).

A modified version of the human pancreatic trypsin inhibitor (PSTI), generated in a protein-design project, has been crystallized in spacegroup P4(3) with lattice constants a = 40.15 A, c = 33.91 A. The structure has been solved by molecular replacement. Refinement of the structure by simulated annealing and conventional restrained least-squares yielded for 8.0 to 2.3 A data a final R-value of 19.1%. Differences to the known structures of porcine PSTI complexed with trypsinogen and modified human PSTI complexed with chymotrypsinogen occur at the flexible N-terminal part of the molecule. These differences are influenced by crystal packing, as are low temperature factors for the binding loop. The geometry of the binding loop is similar to the complexed structures.

Amino Acid Sequence↗
PubMed1993

Variation of the glycosylation of human pancreatic bile-salt-dependent lipase.

Glycoproteins of human pancreatic juice were characterized by means of lectins after electrophoresis and electrotransfer to nitrocellulose membranes. For the detected glycoproteins, only a 100-kDa glycoprotein varied in the pancreatic juice from a normal patient (i.e. without any pancreatic disorder) compared to the pancreatic juice from a patient suffering from chronic pancreatitis. This protein, which is the only protein in human pancreatic juice which is O-glycosylated and N-glycosylated, was identified as the bile-salt-dependent lipase. Among the glycosylated proteins present in human pancreatic juice, only the glycosylation of bile-salt-dependent lipase differs between individuals. The enzyme was isolated either from normal or pathological human pancreatic juices. The purified variants have an identical molecular mass and amino-acid composition. As suspected from lectin affinity studies, the oligosaccharide composition differs between the variants. The structure of the N-linked oligosaccharides of the variant from the pancreatic juice of a normal donor correlated with complete processing and maturation of a complex-type N-glycan. Alteration of the maturation process can be detected for a bile-salt-dependent-lipase variant from a patient suffering with chronic pancreatitis, since the carbohydrate composition is compatible with the predominance of hybrid or high-mannose-type structures. The amount of sugar involved in O-glycosylation associated with the peanut agglutinin reactivity suggests the presence of 12-14 minimal Gal beta 1-->3GalNac-->T/S O-glycan structures which are sialylated and fucosylated. The amount of sugar involved in the O-linked oligosaccharide structure appears to be unchanged in the variants isolated from the pathological pancreatic juice.

Bile Acids and Salts↗
PubMed1982

Carbohydrate structure of the concanavalin A molecular variants of alpha-fetoprotein.

The structure of the carbohydrate units of alpha-fetoprotein from fetal calf serum has been studied. Glycopeptides and oligosaccharides were prepared from alpha-fetoprotein by protease treatment and hydrazinolysis, respectively, and subjected to carbohydrate and amino acid analysis. Two N-glycosidic glycans are present in each alpha-fetoprotein molecule. These were separated into concanavalin A (ConA)-reactive and nonreactive species on ConA-Sepharose. Methylation analysis, Smith degradation, sequential exoglycosidase treatments, and sizing suggested that the major, ConA-nonreactive fraction is composed of triantennary and the minor, ConA-reactive fraction, of biantennary complex-type ConA-reactive and -nonreactive fractions of intact alpha-fetoprotein, respectively, and refractionated on Con A-Sepharose. The results indicate that 75% of alpha-fetoprotein molecules contain two triantennary complex-type glycans, 20% contain one triantennary and one biantennary glycan, and 5% contain two biantennary glycans. The last two molecular variants are bound to ConA. These results explain, at least in part, the previously found heterogeneity of alpha-fetoprotein with respect to charge and molecular size, and provide a biochemical basis for the differing reactivities toward ConA of alpha-fetoprotein from the yolk sac, fetal liver, and various tumors.

Animals↗
PubMed2006

Structure of the inactive variant C60S of Mycobacterium tuberculosis thiol peroxidase.

The genome of Mycobacterium tuberculosis encodes several peroxiredoxins (Prxs) thought to be active against organic and inorganic peroxides. The open reading frame Rv1932 encodes a 165-residue thiol peroxidase (Tpx), which belongs to the atypical 2-Cys peroxiredoxin family. The crystal structure of the C60S mutant of M. tuberculosis Tpx (MtTpx) crystallized in space group P3(1)21, with unit-cell parameters a = 106.08, b = 106.08, c = 65.33 A. The structure has been refined to an R value of 17.1% (R(free) = 24.9%) at 2.1 A resolution. MtTpx is structurally homologous to other peroxiredoxins, including the mycobacterial AhpC and AhpE. The inactive MtTpx C60S mutant structure closely resembles the structure of Streptococcus pneumoniae Tpx (SpTpx) and thus represents the reduced enzyme state. The mutated active-site serine is electrostatically linked to Arg130 and hydrogen bonded to Thr57, practically identical to the cysteine in SpTpx. A cocrystallized acetate molecule mimics the position of the substrate and interacts with Ser60, Arg130 and Thr57.

Amino Acid Substitution↗
PubMed1995

Structural basis of inhibitor affinity to variants of human carbonic anhydrase II.

The activities and structures of certain L198 variants of human carbonic anhydrase II (CAII) have been reported recently [Krebs, J. F., Rana, F., Dluhy, R. A., & Fierke, C. A. (1993) Biochemistry 32, 4496-4505; Nair, S. K., & Christianson, D. W. (1993) Biochemistry 32, 4506-4514]. In order to understand the structural basis of enzyme-inhibitor affinity, we now report the dissociation rate and equilibrium constants for acetazolamide and dansylamide binding to 13 variants of CAII containing substituted amino acids at position 198. These data indicate that inhibitor affinity is modulated by the hydrophobicity and charge of the 198 side chain. Furthermore, we have determined crystal structures of L198R, L198E, and L198F CAIIs complexed with the transition state analog acetazolamide. The substituted benzyl side chain of L198F CAII does not occlude the substrate association pocket, and it is therefore not surprising that this substitution has minimal effects on catalytic properties and inhibitor binding. Nevertheless, the F198 side chain undergoes a significant conformation change in order to accommodate the binding of acetazolamide; the same behavior is observed for the engineered side chain of L198R CAII. In contrast, the engineered side chain of L198E CAII does not alter its conformation upon inhibitor binding. We conclude that the mobility and hydrophobicity or residue 198 side chains affect enzyme-inhibitor (and enzyme-substrate) affinity, and these structure-function relationships are important for understanding the behavior of carbonic anhydrase isozyme III, which bears a wild-type F198 side chain.(ABSTRACT TRUNCATED AT 250 WORDS)

Acetazolamide↗
PubMed2006

An unusual twin-his arrangement in the pore of ammonia channels is essential for substrate conductance.

Amt proteins constitute a class of ubiquitous integral membrane proteins that mediate movement of ammonium across cell membranes. They are homotrimers, in which each subunit contains a narrow pore through which substrate transport occurs. Two conserved histidine residues in the pore have been proposed to be necessary for ammonia conductance. By analyzing 14 engineered polar and non-polar variants of these histidines, in Escherichia coli AmtB, we show that both histidines are absolutely required for optimum substrate conductance. Crystal structures of variants confirm that substitution of the histidine residues does not affect AmtB structure. In a subgroup of Amt proteins, found only in fungi, one of the histidines is replaced by glutamate. The equivalent substitution in E. coli AmtB is partially active, and the structure of this variant suggests that the glutamate side chain can make similar interactions to those made by histidine.

Amino Acid Sequence↗