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At least 757 records · Page 42Linked to original sources
PubMed2002

Structure-function analysis of HscC, the Escherichia coli member of a novel subfamily of specialized Hsp70 chaperones.

Hsp70 chaperones assist protein folding processes through nucleotide-controlled cycles of substrate binding and release. In our effort to understand the structure-function relationship within the Hsp70 family of proteins, we characterized the Escherichia coli member of a novel Hsp70 subfamily, HscC, and identified considerable differences to the well studied E. coli homologue, DnaK, which together suggest that HscC is a specialized chaperone. The basal ATPase cycle of HscC had k(cat) and K(m) values that were 8- and 10,000-fold higher than for DnaK. The HscC ATPase was not affected by the nucleotide exchange factor of DnaK GrpE and stimulated 8-fold by DjlC, a DnaJ protein with a putative transmembrane domain, but not by other DnaJ proteins tested. Substrate binding dynamics and substrate specificity differed significantly between HscC and DnaK. These differences are explicable by distinct structural variations. HscC does not have general chaperone activity because it did not assist refolding of a denatured model substrate. In vivo, HscC failed to complement temperature sensitivity of DeltadnaK cells. Deletion of hscC caused a slow growth phenotype that was suppressed after several generations. Triple knock-outs of all E. coli genes encoding Hsp70 proteins (DeltadnaK DeltahscA DeltahscC) were viable, indicating that Hsp70 proteins are not strictly essential for viability. An extensive search for DeltahscC phenotypes revealed a hypersensitivity to Cd(2+) ions and UV irradiation, suggesting roles of HscC in the cellular response to these stress treatments. Together our data show that the Hsp70 structure exhibits an astonishing degree of adaptive variations to accommodate requirements of a specialized function.

Adenosine Triphosphatases↗
PubMed2005

Klinefelter's syndrome (XXY) as a genetic model for psychotic disorders.

Males with an extra-X chromosome (Klinefelter's syndrome) frequently, although not always, have an increased prevalence of psychiatric disturbances that range from attention deficit disorder in childhood to schizophrenia or severe affective disorders during adulthood. In addition, they frequently have characteristic verbal deficits. Thus, examining brain magnetic resonance imaging (MRI) scans of these individuals may yield clues to the influence of X chromosome genes on brain structural variation corresponding to psychiatric and cognitive disorders. Eleven adult XXY and 11 age matched XY male controls were examined with a structured psychiatric interview, battery of cognitive tests, and an MRI scan. Ten of eleven of the XXY men had some form of psychiatric disturbance, four of whom had auditory hallucinations compared with none of the XY controls. Significantly smaller frontal lobe, temporal lobe, and superior temporal gyrus (STG) cortical volumes were observed bilaterally in the XXY men. In addition, diffusion tensor imaging (DTI) of white matter integrity resulted in four regions of reduced fractional anisotropy (FA) in XXY men compared with controls, three in the left hemisphere, and one on the right. These correspond to the left posterior limb of the internal capsule, bilateral anterior cingulate, and left arcuate bundle. Specific cognitive deficits in executive functioning attributable to frontal lobe integrity and verbal comprehension were noted. Thus, excess expression of one or more X chromosome genes influences both gray and white matter development in frontal and temporal lobes, as well as white matter tracts leading to them, and may in this way contribute to the executive and language deficits observed in these adults. Future prospective studies are needed to determine which gene or genes are involved and whether their expression could be modified with appropriate treatments early in life. Brain expressed genes that are known to escape inactivation on extra-X chromosomes would be prime candidates.

Adult↗
PubMed2001

The dimerization domain of HNF-1alpha: structure and plasticity of an intertwined four-helix bundle with application to diabetes mellitus.

Maturity-onset diabetes mellitus of the young (MODY) is a human genetic syndrome most commonly due to mutations in hepatocyte nuclear factor-1alpha (HNF-1alpha). Here, we describe the crystal structure of the HNF-1alpha dimerization domain at 1.7 A resolution and assess its structural plasticity. The crystal's low solvent content (23%, v/v) leads to tight packing of peptides in the lattice. Two independent dimers, similar in structure, are formed in the unit cell by a 2-fold crystallographic symmetry axis. The dimers define a novel intertwined four-helix bundle (4HB). Each protomer contains two alpha-helices separated by a sharp non-canonical turn. Dimer-related alpha-helices form anti-parallel coiled-coils, including an N-terminal "mini-zipper" complementary in structure, symmetry and surface characteristics to transcriptional coactivator dimerization cofactor of HNF-1 (DCoH). A confluence of ten leucine side-chains (five per protomer) forms a hydrophobic core. Isotope-assisted NMR studies demonstrate that a similar intertwined dimer exists in solution. Comparison of structures obtained in multiple independent crystal forms indicates that the mini-zipper is a stable structural element, whereas the C-terminal alpha-helix can adopt a broad range of orientations. Segmental alignment of the mini-zipper (mean pairwise root-mean-square difference (rmsd) in C(alpha) coordinates of 0.29 A) is associated with a 2.1 A mean C(alpha) rmsd displacement of the C-terminal coiled-coil. The greatest C-terminal structural variation (4.1 A C(alpha) rmsd displacement) is observed in the DCoH-bound peptide. Diabetes-associated mutations perturb distinct structural features of the HNF-1alpha domain. One mutation (L12H) destabilizes the domain but preserves structural specificity. Adjoining H12 side-chains in a native-like dimer are predicted to alter the functional surface of the mini-zipper involved in DCoH recognition. The other mutation (G20R), by contrast, leads to a dimeric molten globule, as indicated by its 1H-NMR features and fluorescent binding of 1-anilino-8-naphthalene sulfonate. We propose that a glycine-specific turn configuration enables specific interactions between the mini-zipper and the C-terminal coiled-coil.

Amino Acid Sequence↗
PubMed1987

Genetic variation in the human hepatic cytochrome P-450 system.

Studies in rodents indicate that the cytochrome P-450 system consists of a superfamily of heme proteins, produced by clusters of structural genes on different chromosomes. Equivalent P-450s of different species show more homologies than members of different P-450 families within a species. The Ah receptor serves the induction of members of one of the cytochrome families. The human structural gene for the methylcholanthrene-inducible P1-450 is located on Chromosome 15. This gene has been completely sequenced. The human Ah receptor is also measurable. New methods to measure inducibility in man involve new lymphocyte bioassays and mRNA determinations, while in vivo biotransformation studies of caffeine allow estimates of the state of induction. Structural genes for phenobarbital-inducible cytochromes have been localized to Chromosome 19. The deficiency of biotransformation of debrisoquine and sparteine continues to be explored intensely. Linkage studies indicate the gene for the variable cytochrome P-450 to be located on Chromosome 22. The deficiency is more likely due to structural variation than absence of the cytochrome. Inhibiting drugs can mimic the genetic defect. Many pharmacological and toxicological consequences of the deficiency have been defined. The main characteristics of the genetic deficiencies affecting the metabolisms of mephenytoin, phenytoin, tolbutamide, nifedipine and of methyl cysteine were outlined briefly.

Animals↗
PubMed2004

The tryptophan switch: changing ligand-binding specificity from type I to type II in SH3 domains.

The ability of certain Src homology 3 (SH3) domains to bind specifically both type I and type II polyproline ligands is perhaps the best characterized, but also the worst understood, example in the family of protein-interaction modules. A detailed analysis of the structural variations in SH3 domains, with respect to ligand-binding specificity, together with mutagenesis of SH3 Fyn tyrosine kinase, reveal the structural basis for types I and II binding specificity by SH3 domains. The conserved Trp in the SH3 binding pocket can adopt two different orientations that, in turn, determine the type of ligand (I or II) able to bind to the domain. The only exceptions are ligands with Leu at positions P(-1) and P(2), that deviate from standard poly-Pro angles. The motion of the conserved Trp depends on the presence of certain residues located in a key position (132 for Fyn), near the binding pocket. SH3 domains placing aromatic residues in this key position are promiscuous. By contrast, those presenting beta-branched or long aliphatic residues block the conserved Trp in one of the two possible orientations, preventing binding in a type I orientation. This is experimentally demonstrated by a single mutation in Fyn SH3 (Y132I) that abolishes type I ligand binding, while preserving binding to type II ligands. Thus, simple conformational changes, governed by simple rules, can have profound effects on protein-protein interactions, highlighting the importance of structural details to predict protein-protein interactions.

Amino Acid Sequence↗
PubMed2005

In situ observation of CO oxidation on Ag110(2 x 1)-O by scanning tunneling microscopy: structural fluctuation and catalytic activity.

On the added-row reconstructed Ag(110)(nx1)-O surfaces where one-dimensional -Ag-O-Ag-O- chains arrange periodically, the clean-off reaction of O adatoms by CO was investigated using variable temperature scanning tunneling microscopy (VT-STM). Based on the in situ STM observations of the surface structure variation in the course of the reaction at various temperatures, we found that the reaction kinetics are significantly affected by the structural transition of AgO chains from a solid straight line configuration to dynamically fluctuating configurations. Below 230 K where the chains are straight, the reaction takes place only at the end of the chains, so that the reaction progresses in the zero-order kinetics with the reaction front propagating along the chain. The temperature dependence of the reaction rates yields the activation barrier of 41 kJ/mol and the preexponential factor of 1.7 x 10(3) cm(-2) s(-1). At room temperature, the reaction rate is drastically accelerated when almost half of the O adatoms are eliminated and the chains start fluctuating. The dynamic formation of active sites equivalent to the end of chains upon the chain fluctuation results in the nonlinear increase of the reaction rate.

Journal Article↗
PubMed2026

SIVA: diagonal integration of spatial multi-omics data via spatially informed variational autoencoders and anchor guidance.

MOTIVATION: Understanding cellular states and regulatory programs requires integrative analysis of multiple omics layers. Although recent spatial sequencing technologies allow molecular profiling of cells within their tissue context, paired spatial multi-omics assays are still limited by technical complexity and cost. This creates a pressing need for diagonal integration methods that enable joint analysis of unpaired spatial omics datasets. RESULTS: We propose SIVA, a deep generative framework based on Spatially-Informed Variational Autoencoders with Anchor Guidance, for diagonal integration of spatial multi-modal data. SIVA employs modality-specific variational autoencoders (VAEs) with a hybrid latent embedding that integrates Gaussian process and standard Gaussian priors, enabling joint modeling of spatially structured variation and dominant underlying data distributions across modalities. To facilitate cross-modal alignment in the absence of one-to-one cell correspondence, SIVA adopts a dual integration strategy combining global distribution alignment via Maximum Mean Discrepancy and local correspondence guidance using mutual nearest neighbor anchors. Extensive experiments across multiple cross-slice integration scenarios demonstrate that SIVA achieves robust and accurate integration of unpaired spatial omics datasets, consistently outperforming existing methods. AVAILABILITY AND IMPLEMENTATION: The source codes are available at https://github.com/PelenJiang/SIVA.

Autoencoder↗
PubMed1994

Analysis of the structure of Pseudomonas glumae lipase.

The lipase produced by Pseudomonas glumae is monomeric in the crystalline state and has a serine protease-like catalytic triad; Ser87-His285-Asp263. The largest domain of the protein resembles closely a subset of the frequently observed alpha/beta-hydrolase fold and contains a well-defined calcium site. This paper describes structural analysis of this protein, focusing on (i) structural comparison with the lipase from Geotrichum candidum, (ii) the probable nature of the conformational change involved in substrate binding and (iii) structural variations amongst the family of Pseudomonas lipases. This analysis reveals similarities between P. glumae lipase and G. candidum lipase involving secondary structural elements of the hydrolase core and the loops carrying the catalytic serine and histidine residues. A possible functional equivalence has also been identified between parts of the two molecules thought to be involved in a conformational change. In addition, determination of the structure of P. glumae lipase has allowed rationalization of previously reported protein engineering experiments, which succeeded in improving the stability of the enzyme with respect to proteolysis.

Amino Acid Sequence↗
PubMed1986

Influence of glycosylation on allelic and cell-specific Mr variation, receptor processing, and ligand binding of the human complement C3b/C4b receptor.

The human complement C3b/C4b receptor (CR1), a single chain membrane glycoprotein of Mr approximately 200,000, has several cell-specific Mr variations as well as an allelic variation involving four phenotypes whose Mr values span a range of 90,000. We investigated the role of glycosylation in these structural variations and in receptor metabolism. In the human HL-60 promyelocytic leukemic cell line differentiated toward granulocytes or monocytes and in Epstein-Barr virus-transformed B lymphoblastoid cell lines of the common phenotype, CR1 is synthesized as a precursor of Mr = 222,000 that is converted into mature CR1s with differing Mr values. Endoglycosidase F treatment of mature CR1 from all these cell types produced the same lower Mr band. Additionally, the previously noted 5,000 higher Mr of CR1 from human peripheral granulocytes versus erythrocytes was abrogated by endoglycosidase F. Hence these cell-specific variations are due to differences in N-glycosylation. Lectin affinity chromatography shows that these N-linked oligosaccharides are mostly tri- and tetraantennary complex-type species with specific differences in fractionation patterns that correlate with their differing Mrs. In lymphoblastoid cell lines, the four allelic variants each have a precursor 6,000 lower in Mr than the respective mature CR1. In the presence of tunicamycin, each of the CR1 allelic products is 25,000 lower in Mr than the glycosylated receptor. The failure to radiolabel CR1 with [3H]glucosamine in the presence of tunicamycin indicates the lack of O-linked oligosaccharide on CR1. These data, taken together, strongly suggest that the CR1 polymorphism resides at the polypeptide level. Nonglycosylated CR1 synthesized in the presence of tunicamycin had twice the turnover rate of glycosylated CR1. The efficiency of surface membrane insertion and of ligand binding to hemolytically inactive C3 were markedly reduced for nonglycosylated CR1, suggesting that glycosylation is important for the proper expression of CR1 function.

Alleles↗
PubMed1991

Variations in the cytoskeletal interaction and posttranslational modification of the CD44 homing receptor in macrophages.

Murine CD44 is a cell surface glycoprotein that is thought to play a role in leukocyte migration. We studied the structure and expression of CD44 on two populations of macrophages: those that reside in the peritoneum of unprimed mice, and those that have been elicited to migrate into the peritoneum by the intraperitoneal injection of agents that cause localized inflammatory responses. Our studies reveal structural variations in both the extracellular and intracellular domains of CD44 expressed by these two macrophage populations. The form of CD44 in elicited macrophages has an apparent molecular mass that is approximately 5 kD greater and more heterogenous than that in resident macrophages. This structural changes is posttranslational, extracellular, and apparently reflects increases in N-linked glycosylation. It is also specific for CD44 and does not occur with several other glycoproteins examined. This novel regulation of glycosylation may play an important role in the ability of CD44 to bind to different substrates, particularly lectin-like ligands. In addition, we demonstrate that CD44 in resident macrophages is divided into two pools, one containing nonphosphorylated, cytoskeletally associated CD44, and one containing phosphorylated, unassociated CD44. In contrast, CD44 on the surface of elicited macrophages does not associate with the cytoskeleton. The attachment of CD44 to the cytoskeleton involves either direct or indirect association with actin. The regulated association of CD44 with the cytoskeleton suggests that it may influence or be influenced by macrophage mobility.

Animals↗
PubMed1991

Genetic studies of human apolipoproteins. XVI. APOE polymorphism and cholesterol levels in the Mayans of the Yucatan Peninsula, Mexico.

Structural variation at the APOE locus is a major determinant of interindividual differences in cholesterol levels in populations at large. We have determined APOE structural polymorphism and estimated its impact on total cholesterol in the Mayans of the Yucatan Peninsula from Mexico. A unique pattern of APOE allele frequency distribution was observed, with no example of the APOE*2 allele and a relatively low incidence (9%) of the APOE*4 allele, giving rise to the lowest average heterozygosity at the APOE locus observed to date. The reported elevating affect of the APOE*4 allele on cholesterol has been found to be absent in the Mayans; several possible explanations which may account for the absence of this affect are discussed. In addition to APOE the gene products of five other apolipoprotein loci were screened and low frequency variation, possibly due to European admixture, was observed in two systems (APOH and APOA-IV).

Alleles↗
PubMed1997

An experimental study of the reflection from spherical and flat ended cylindrical targets suitable for fetal Doppler performance assessment.

The performance of small-diameter targets suitable for use as oscillating targets for testing the sensitivity of Doppler fetal heartbeat detectors has been systematically studied. Experimental results are presented in the 1.6-3.0 MHz frequency range for the plane-wave reflection loss for a total of 16 targets: spherical balls made of stainless steel; hemispherical-ended rods made of PTFE; and flat-ended rods made of stainless steel, PTFE, polycarbonate, and tungsten carbide. Results show that the fine-structure variation of reflection loss with frequency is greatest in the case of spherical ball targets and least for flat-ended targets. It has been shown that, providing care is taken during manufacture, the reflection loss from a flat-ended target can be predicted using a simple theory based on a plane disc reflector. Tungsten carbide targets consisting of a long rod with a diameter of 1.6 mm tapered down to a cylindrical flat end with a diameter of 0.4, 0.5, and 0.6 mm have been shown to provide reflection losses of between 60 and 40 dB, and to have a smooth variation of reflection loss with frequency. They can also be manufactured in a form that allows no significant interference from the supporting structure and, therefore, are ideal targets to meet the requirements of International Electrotechnical Commission 1266:1995.

Doppler Effect↗
PubMed1999

Design, synthesis, and biological evaluation of novel non-piperazine analogues of 1-[2-(diphenylmethoxy)ethyl]- and 1-[2-[bis(4-fluorophenyl)methoxy]ethyl]-4-(3-phenylpropyl)piperazines as dopamine transporter inhibitors.

A series of novel diamine, amine-amide, and piperazinone analogues of N-[2-(bisarylmethoxy)ethyl]-N'-(phenylpropyl)piperazines, GBR 12909 and 12935, were synthesized and evaluated as inhibitors of presynaptic monoamine neurotransmitter transporters. The primary objective of the study was to determine the structural requirements for selectivity of ligand binding and potency for neurotransmitter reuptake inhibition. In general, the target compounds retained transporter affinity; however, structural variations produced significant effects on reuptake inhibition and transporter selectivity. For example, analogues prepared by replacing the piperazine ring in the GBR structure with an N, N'-dimethylpropyldiamine moiety displayed enhanced selectivity for binding and reuptake inhibition at the norepinephrine (NE) transporter site (e.g. 4 and 5). Congeners in which the amide nitrogen atom was attached to the aralkyl moiety of the GBR molecule showed moderate affinity (K(i) = 51-61 nM) and selectivity for the dopamine transporter (DAT) site. In contrast, introduction of a carbonyl group adjacent to either nitrogen atom of the piperazine ring (e.g. 25 and 27) was not well tolerated. From the compounds prepared, analogue 16 was selected for further evaluation. With this congener, locomotor activity induced by cocaine at a dose of 20 mg/kg was attenuated with an AD(50) (dose attenuating cocaine-induced stimulation by 50%) of 60.0 +/- 3.6 mg/kg.

Amides↗
PubMed1991

Comparison of the cartilage proteoglycan core protein synthesized by chondrocytes of different ages.

Chondrocytes of different ages synthesize proteoglycans which have structural differences in both the chondroitin sulfate and keratan sulfate glycosaminoglycans. In order to ascertain whether age-dependent differences also occur in the core protein, the chick limb bud mesenchymal cell culture system was utilized to analyze newly synthesized proteoglycan core protein from undifferentiated mesenchymal cells (day 1 and 2), newly differentiated cartilage (day 4), mature cartilage (day 8), and senescent cartilage (day 16). The core protein synthesized at various times was identified by radiolabeling with [3H]leucine and [35S]sulfate immediately prior to extraction and purification. The sizes of the various core protein preparations were compared by electrophoresis on a 3% polyacrylamide gel after partial deglycosylation with chondroitinase AC and keratanase. The proteoglycans from day 4, 8, and 16 cultures each give rise to a single band of approximately 475,000 daltons. The proteoglycans from day 1 and 2 cultures also give rise to the 475,000 dalton band, but each contains several other components which produce a smear of high molecular weight material on the gel. The monomer proteoglycans were incubated with cyanogen bromide and the resultant peptides separated by electrophoresis on a 5-17.5% polyacrylamide gel. The peptide displays of core proteins synthesized on days 4, 8 and 16 are virtually identical in terms of the number and electrophoretic distribution of the core protein peptides. In contrast, proteoglycan core proteins from day 1 and day 2 cultures give rise to peptide displays which resemble those from older cultures in some respects but have distinct features as well. The absence of structural variation in the newly synthesized proteoglycan core proteins from cartilage of different ages suggests that the age-related changes in the structure of the intact proteoglycans result from differences in the glycosaminoglycan biosynthetic machinery rather than alterations in the acceptor molecule (i.e., the core protein).

Aggrecans↗
PubMed2002

Genetic polymorphism of the human ICOS gene.

Inducible costimulator (ICOS) is a novel receptor belonging to the same family as CD28 and CTLA4, which regulate T-lymphocyte activation in the immune response. The genes for these molecules are located adjacent to each other on Chromosome 2q33. Many autoimmune diseases have been found to be genetically linked to or associated with genetic markers near the CTLA4 gene. However, as all three genes are closely linked and have related functions, it is possible that the findings could be explained by variation in CD28 or ICOS. Few data on genetic variation in the ICOS gene are available. We sequenced the ICOS gene in 13 healthy unrelated individuals and found eight single nucleotide polymorphisms. One was located in the first intron, and the others in the untranslated region of the last exon. The allele frequencies and linkage disequilibrium were determined from a population sample of 63 Finnish individuals. The results show that the ICOS gene is polymorphic, but no variation in the coding sequence was detected, implying that the genetic linkage of this gene region to autoimmune diseases may not result from structural variation in the ICOS molecule. These polymorphisms, however, should be useful in genetic studies of this candidate gene.

Abatacept↗
PubMed2001

Hydrolysis theory for cisplatin and its analogues based on density functional studies.

Hydrolysis of cisplatin, the most widely used anticancer drug in the world, is believed to be the key activation step before the drug reaching its intracellular target DNA. To obtain an accurate hydrolysis theory for this important class of square-planar Pt(II) complexes, three typical reactions, i.e., the first and second hydrolyses of cisplatin and the hydrolysis of [Pt(dien)Cl](+) (dien = diethylenetriamine), were studied at the experimental temperature with the solvent effect using mPW1PW91/SDD from a comprehensive methodological study on the Hartree-Fock (HF) ab initio method, electron correlation methods, pure density functional theory (DFT) methods, and hybrid HF-DFT methods with several basis sets. The true five stationary states in the second-order nucleophilic substitution (S(N)2) pathway for the hydrolysis process, namely, reactant (R) --> intermediate 1 (I1) --> TS --> intermediate 2 (I2) --> product (P) were obtained and characterized theoretically for the first time. The most remarkable structural variations and the associated atomic charge variations in the hydrolysis process were found to occur in the equatorial plane of the five-coordinate trigonal-bipyramidal (TBP)-like structures of I1, TS, and I2. The reaction with the TS structure of smaller L-M-E angle and more lengthened M-L and M-E bonds was found to have a smaller Gibbs free energy change and accordingly the better hydrolysis yield. It is found that the sum of the three concentric angles in the TBP's equator is near 360 degrees in I1 and I2 and is almost 360 degrees in TS in each reaction. The associated energy profiles again demonstrated a typical S(N)2 reaction curve. The computed forward and backward reaction enthalpy (Delta H(++)) and reaction entropy (Delta S(++)) in the rate-determining step I1 --> TS --> I2 are in good agreement with the experiments. Natural bonding orbital population analysis shows that the charge-separating extent follows the same order of Delta G in studied reactions. Comparing with the computational results of gas-phase reactions, it can be concluded that the solvent effect should be considered to obtain an accurate hydrolysis picture. The most affected structural parameters after solvation are related to the equatorial plane of the TBP-like geometry. The results provide theoretical guidance on detailed understanding on the mechanism of the hydrolysis of cisplatin, which could be useful in the design of novel Pt-based anticancer agents.

Antineoplastic Agents↗
PubMed1993

Morphological variations of the human ascending aortic fold.

The ascending aortic fold, a fibrofatty epicardial fold embracing the middle part of the human ascending aorta, was studied in 90 black South African hearts for structural variation. The fold was present in all specimens. It was oblique in 51 cases, horizontal in 17, vertical in 2, oval in 2, horizontal-oblique in 4, vertical-oblique in 6, vertical-horizontal in 3, vertical-horizontal-oblique in 1 and oval-oblique in 1. The oblique form corresponds to the 'classic' form described in the literature.

Adolescent↗
PubMed2001

Yet another numbering scheme for immunoglobulin variable domains: an automatic modeling and analysis tool.

A common residue numbering scheme for all immunoglobulin variable domains (immunoglobulin light chain lambda (V(lambda)) and kappa (V(kappa)) variable domains, heavy chain variable domains (V(H)) and T-cell receptor alpha (V(alpha)), beta (V(beta)), gamma (V(gamma)) and delta (V(delta)) variable domains) has been devised. Based on the spatial alignment of known three-dimensional structures of immunoglobulin domains, it places the alignment gaps in a way that minimizes the average deviation from the averaged structure of the aligned domains. This residue numbering scheme was applied to the immunoglobulin variable domain structures in the PDB database to automate the extraction of information on structural variations in homologous positions of the different molecules. A number of methods are presented that allow the automated projection of information derived from individual structures or from the comparison of multi-structure alignments onto a graphical representation of the sequence alignment.

Amino Acid Sequence↗