Structure-function Information Research Articles

BIOKDD 2005 workshop report

Bioinformatics is the science of managing, mining, and interpreting information from biological entities. Genome sequencing projects have contributed to an exponential growth in complete and partial sequence databases. The structural genomics initiative aims to catalog the structure-function information for proteins. Advances in technology such as microarrays have launched the subfield of genomics and proteomics to study the genes, proteins, and the regulatory gene expression circuitry inside the cell. What characterizes the state of the field is the flood of data that exists today or that is anticipated in the future; data that needs to be mined to help unlock the secrets of the cell. Knowledge extracted from such analysis can be used effectively to better design new drugs, offer better medical care via diagnostic tests that combine information from multiple sources, and improve scientific and clinical practice.

Influence of Disaccharide Structure on Prebiotic Selectivity in Vitro

To obtain structure-function information of a range of carbohydrates, which are available only in very small quantities, an in vitro fermentation method using 7 mg of carbohydrate, 0.7 mL of basal medium, and 1% (w/v) of fecal bacteria was validated against a pH-controlled batch culture with 150 mL of basal medium and 1.5 g of test carbohydrate. This method was used to determine the influence of different glycosidic linkages and monosaccharide compositions of disaccharides on the selectivity of microbial fermentation. A prebiotic index (PI) was calculated for each disaccharide. Generally, disaccharides with linkages of 1-2, 1-4, and 1-6 generated a high PI score, with kojibiose and sophorose showing the greatest values (21.62 and 18.63, respectively). Apart from 6alpha-mannobiose, mannose-containing disaccharides gave a low PI due to low numbers of bifidobacteria and lactobacilli and an increase in bacteroides. The structure-function information obtained in this study may lead to a predictive understanding of how specific structures are fermented by the human gut microflora.

Report on BIOKDD04

BIOKDD'04 was held in conjunction with the 10th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, in Seattle, WA, in August 2004. There are numerous sources of biological data that provides challenging opportunities for data mining. For example, the structural genomics initiative aims to catalog the structure-function information for proteins. Advances in technology such as microarrays have launched the subfield of genomics and proteomics to study the genes, proteins, and the regulatory gene expression circuitry inside the cell. Other sources of data include the rapidly growing literature in bioinformatics (e.g., PubMed), the data on biochemical pathways, the evolutionary relationships among organisms in the Tree of Life, high throughput drug design combinatorial libraries, and so on. In addition to the data from biology and genomics, there are rich sources of data from other biosciences, including biomedical, and neuroscience data.

Development of response-selective agonists of human C5a anaphylatoxin: conformational, biological, and therapeutic considerations.

Numerous studies on the relationship between the structure and function of peptide agonists derived from the biologically active, C-terminal region of human C5a anaphylatoxin have been reported over the past decade. These studies have been performed with the objective of parlaying this structure-function information into the design of peptide/peptidomimetic modulators of C5a receptor (C5aR)-mediated function. In this review, we describe a rational approach for the development of conformationally biased, decapeptide agonists of C5a and described how these stabilized and specific conformational features relate to the expression of specific C5a-like activities in vitro and in vivo. The therapeutic potential of such response-selective C5a agonists is discussed and underscored by the results of one such response-selective C5a agonist that was used in vivo as an effective molecular adjuvant capable of generating antigen-specific humoral and cellular immune responses. Finally, we describe the synthesis of a new generation of highly response-selective, conformationally biased C5a agonist and discuss the in vitro and in vivo biologic results that so indicate this biologic selectivity.

A physical-space version of the stretched-vortex subgrid-stress model for large-eddy simulation

A physical-space version of the stretched-vortex subgrid-stress model is presented and applied to large-eddy simulations of incompressible flows. This version estimates the subgrid-kinetic energy required for evaluation of the subgrid-stress tensor using local second-order structure-function information of the resolved velocity field at separations of order the local cell size. A relation between the structure function and the energy spectrum is derived using the kinematic assumptions of the stretched-vortex model for locally homogeneous anisotropic turbulence. Results of large-eddy simulations using this model are compared to experimental and direct numerical simulation data. Comparisons are shown for the decay of kinetic energy and energy spectra of decaying isotropic turbulence and for mean velocities, root-mean-square velocity fluctuations and turbulence-kinetic energy balances of channel flow at three different Reynolds numbers.

Generation of up-regulated allosteric variants of potato ADP-glucose pyrophosphorylase by reversion genetics

Mutagenesis of the large subunit (LS) of the potato ADP-glucose pyrophosphorylase generated an enzyme, P52L, that was insensitive to 3-phosphoglycerate (3-PGA). To identify additional residues involved in 3-PGA interaction, we subjected P52L LS DNA to a second round of mutagenesis and identified second-site revertants by their ability to restore glycogen accumulation as assessed by iodine (I2) staining. Enzymes from class I revertants with normal I2-staining had an 11- to 49-fold greater affinity for the activator 3-PGA compared with the P52L mutant and a decreased sensitivity to the inhibitor orthophosphate. Sequence analysis of these class I revertants identified a P66L mutation in R4, an E38K mutation in R20, and a G101N mutation in R10 and R32. These mutations appear to restore 3-PGA binding by counteracting the effect of the P52L mutation because introducing E38K or G101N into the wild-type LS led to enzyme variants with higher affinity for the activator 3-PGA and increased resistance to the inhibitor orthophosphate. The generation of these revertant enzymes provides additional structure-function information on the allosteric regulation of higher plant ADP-glucose pyrophosphorylases and validates a strategy for developing novel variants of the enzyme that may be useful in manipulating starch biosynthesis in higher plants.

Neonatal, Lethal Noncompaction of the Left Ventricular Myocardium Is Allelic with Barth Syndrome

Loss-of-function mutations in the G4.5 gene have been shown to cause Barth syndrome (BTHS), an X-linked disorder characterized by cardiac and skeletal myopathy, short stature, and neutropenia. We recently reported a family with a severe X-linked cardiomyopathy described as isolated noncompaction of the left ventricular myocardium (INVM). Other findings associated with BTHS (skeletal myopathy, neutropenia, growth retardation, elevated urinary organic acids, and mitochondrial abnormalities) were either absent or inconsistent. A linkage study of the X chromosome localized INVM to the Xq28 region near the BTHS locus, suggesting that these disorders are allelic. We screened the G4.5 gene for mutations in this family with SSCP and direct sequencing and found a novel glycine-to-arginine substitution at position 197. This position is conserved in a homologous Caenorhabditis elegans protein. We conclude that INVM is a severe allelic variant of BTHS with a specific effect on the heart. This finding provides further structure-function information about the G4.5 gene product and has implications for unexplained cases of severe infantile hypertrophic cardiomyopathy in males.

Novel human DNA alkyltransferases obtained by random substitution and genetic selection in bacteria.

DNA repair alkyltransferases protect organisms against the cytotoxic, mutagenic, and carcinogenic effects of alkylating agents by transferring alkyl adducts from DNA to an active cysteine on the protein, thereby restoring the native DNA structure. We used random sequence substitutions to gain structure-function information about the human O6-methylguanine-DNA methyltransferase (EC 2.1.1.63), as well as to create active mutants. Twelve codons surrounding but not including the active cysteine were replaced by a random nucleotide sequence, and the resulting random library was selected for the ability to provide alkyltransferase-deficient Escherichia coli with resistance to the methylating agent N-methyl-N'-nitro-N-nitrosoguanidine. Few amino acid changes were tolerated in this evolutionarily conserved region of the protein. One mutation, a valine to phenylalanine change at codon 139 (V139F), was found in 70% of the selected mutants; in fact, this mutant was selected much more frequently than the wild type. V139F provided alkyltransferase-deficient bacteria with greater protection than the wild-type protein against both the cytotoxic and mutagenic effects of N-methyl-N'-nitro-N-nitrosoguanidine, increasing the D37 over 4-fold and reducing the mutagenesis rate 2.7-5.5-fold. This mutant human alkyltransferase, or others similarly created and selected, could be used to protect bone marrow cells from the cytotoxic side effects of alkylation-based chemotherapeutic regimens.

Characterization of mutant rhodopsins responsible for autosomal dominant retinitis pigmentosa. Mutations on the cytoplasmic surface affect transducin activation

Rhodopsin mutants responsible for autosomal dominant retinitis pigmentosa (ADRP) were prepared by site-directed mutagenesis and characterized. The aim was to evaluate ADRP mutations that occur at three locations on the cytoplasmic surface of rhodopsin: Thr-58 near the cytoplasmic border of helix A, the tetrapeptide Leu-68 to Pro-71 in the first cytoplasmic loop, and Arg-135 at the cytoplasmic border of helix C. It was hypothesized that amino acid changes at these sites would result in mutant rhodopsins with normal spectral properties but defects in their ability to interact with the rod outer segment G protein, transducin. A set of 12 mutant opsin genes was prepared. Four of the mutants were known to cause ADRP: Thr-58 replaced by Arg, a four-amino acid deletion (Leu-68/Arg-69/Thr-70/Pro-71), Arg-135 replaced by Leu, and Arg-135 replaced by Trp. Eight additional mutants were prepared to provide complementary structure-function information. The four-amino acid deletion mutant failed to bind 11-cis-retinal. However, each of the Thr-58 and Arg-135 mutants bound 11-cis-retinal to form a pigment with a visible absorbance maximum (lambda max) of 500 nm. Upon illumination, each pigment was converted to a metarhodopsin II-like spectral form (lambda max = 380 nm). However, each of these spectrally normal ADRP mutants was defective in activating guanine nucleotide exchange by transducin. These results identify a defect in the signal transduction pathway in spectrally normal mutant rhodopsins that cause ADRP.

Vitamin D: structure-function analyses and the design of analogs.

There is continuing and emerging new interest in the development of vitamin D analogs resulting from the recognition that analogs of 1 alpha,25-dihydroxyvitamin D3 [1 alpha,25-(OH)2D3] may be therapeutically useful. Side chain analogs of this steroid hormone are of particular interest because a family of lead structures have recently emerged for possible use in the treatment of certain types of cancers and skin diseases. Because of the chaotic array of side chain structures which exhibit useful therapeutic indices for these purposes, a more systematic approach towards developing intelligible structure-function information needs development. Accordingly, a method has been devised to analyze analogs as to their side chain topology based on identifying specific occupancy volumes through conformational analysis. Dot maps have been constructed as an indication of the volume in space which the side chain of 1 alpha,25-(OH)2-D3 or analogs is permitted to occupy. Volume exclusion analyses based on comparison of structural and biological data for 1 alpha,25-(OH)2-D3 and analogs are anticipated to lead to a more cogent model for drug design. A cautionary note on the limitations of this approach is discussed.

In vitro expression and site-specific mutagenesis of the cloned human lipoprotein lipase gene. Potential N-linked glycosylation site asparagine 43 is important for both enzyme activity and secretion.

Detailed structure-function information about human lipoprotein lipase (LPL) is unavailable because it is difficult to purify large amounts of the enzyme for study. To circumvent this problem, we constructed an in vitro LPL expression vector. Human LPL cDNA was cloned and inserted into the expression vector p91023(B). After transfection of COS M-6 cells with the human LPL cDNA construct, LPL enzyme activity was detected in cell extracts and culture medium. Purified human apolipoprotein C-II caused a 5-fold stimulation of the recombinant human LPL expressed in vitro. Using site-specific mutagenesis, Ala residues were substituted for Asn residues at two potential N-linked glycosylation sites (positions 43 and 359) and at a third unrelated Asn (position 257) in the LPL cDNA. RNA blot analysis demonstrated the presence of a single mRNA species in COS cells transfected with wild-type and mutant LPL expression vectors. Intracellular and secreted LPL activity was absent in the construct containing an Ala for Asn mutation at position 43, whereas the same substitutions at positions 257 and 359 did not appreciably affect activity. LPL activity was also absent in another construct containing a Gln for Asn mutation at position 43. Quantitation of LPL protein mass concomitant with measurement of enzyme activity showed that substitution of Ala or Gln for Asn at position 43 resulted in the production of an enzymatically inactive protein which accumulated intracellularly but was not secreted into the culture medium. Our report represents an initial documentation of the expression of cloned human LPL in vitro and of the importance of Asn-43 for both enzyme activity and secretion.

Towards a structural-functional classification of fynbos: a comparison of methods

The need for a classification of the vegetation of the fynbos region is stressed. In the present work we have evaluated some structural-functional approaches that could be used to classify and describe fynbos. A priori and a posteriori approaches to classification are reviewed. The a posteriori approach appears to be superior.Test data derived from 21 plots from a range of fynbos types were used to test some methods of collecting and analysing structural-functional information for an a posteriori classification. With respect to data collection, no single method was superior. However, a major improvement on our methodology would be possible if the growth-form system used were to be extended. The classifications that were erected were produced by means of computer-based numerical methods. These methods are essential if large data sets are to be analysed. However, the structural-functional classifications produced by numerical methods should only be regarded as working hypotheses; refinement of the classifications should proceed by intuitive methods. We feel that the a posteriori approach, even though it has its problems, will provide a suitable methodology for an ecologically meaningful classification of fynbos vegetation.