How fatty acids bind to proteins: the inside story from protein structures

The interactions of fatty acids with proteins have been probed with a great variety of techniques and strategies. Many approaches have substituted covalently labeled fatty acids or structurally related molecules. Information from such studies ultimately requires validation by studies with natural fatty acids. However, even the best conventional approaches with natural fatty acids generally have revealed only limited aspects of fatty acid-protein interactions. In contrast, recent crystallographic and NMR studies of several proteins with bound fatty acids provide complete three-dimensional structures with molecular details of these interactions. This presentation reviews three examples of proteins that are indirectly or directly involved in cell signaling: a protein in the plasma compartment (human serum albumin); a protein family in the cytosolic compartment of mammalian cells (fatty-acid-binding proteins), and a nuclear protein (peroxisome proliferator-activated receptor): it also discusses the structures of these proteins and their binding pocket(s), compares their specific modes of interactions with fatty acids, and discusses established and potential roles of fatty acid-protein interactions in cell signaling.     

SR-BI is required for microvillar channel formation and the localization of HDL particles to the surface of adrenocortical cells in vivo

Scavenger receptor class B type I (SR-BI) mediates the selective uptake of HDL cholesteryl ester into liver and steroidogenic tissues. In steroidogenic cells, juxtaposed microvilli, or microvilli snuggled against the plasma membrane create microvillar channels that fill with HDL. Microvillar membranes contain SR-BI and are believed to be the site of HDL cholesteryl ester uptake. A recent study showed that SR-BI expression in insect cells elicits membrane structures that contain SR-BI, bind HDL, and closely resemble the ultrastructure of microvillar channels. In the present study we compared the ultrastructure of adrenal gland microvillar membranes in Srb1+/+ and Srb1-/- mice to test whether SR-BI is required for the formation of microvillar channels. The results show that SR-BI is absolutely required for microvillar channel formation and that the microvillar membranes of Srb1-/- mice are 17% thinner than in Srb1+/+ mice.We conclude that SR-BI has a major influence on plasma membrane ultrastructure and organization in vivo.     

Interactions of very long-chain saturated fatty acids with serum albumin

The remarkable binding properties of serum albumin have been investigated extensively, but little is known about an important class of fatty acids, the very long-chain saturated fatty acids (VLCFA; >18 carbons). Although VLCFA are metabolized efficiently in normal individuals, they are markers for and possibly causative agents of several peroxisomal disorders. We studied the binding of [(13)C]carboxyl-enriched arachidic (C20:0), behenic (C22:0), lignoceric (C24:0), and hexacosanoic (C26:0) acids to bovine serum albumin (BSA) by (13)C-NMR spectroscopy. For each VLCFA, the NMR spectra showed multiple signals at chemical shifts previously identified for long-chain fatty acids (12-18 carbons), suggesting stabilization of binding by similar, if not identical, interactions of the fatty acid carboxyl anion with basic amino acid residues. The maximal binding (mol of VLCFA/mol of BSA) and the number of observed binding sites decreased with increasing chain length, from 4-5 for C20:0, 3-4 for C22:0, and 2 for C24:0; we validated our previous conclusion that BSA has only one site for C26:0 (Ho, J. K., H. Moser, Y. Kishimoto, and J. A. Hamilton. 1995. J. Clin. Invest. 96: 1455-1463). Analysis of chemical shifts suggested that the highest affinity sites for VLCFA are low affinity sites for long-chain fatty acids. In competition experiments with (13)C-labeled C22:0 (3 mol/mol of BSA) and unlabeled oleic acid, C22:0 bound to BSA in the presence of up to 4 mol of oleic acid/mol of BSA, but 1 mol was shifted into a different site. Our studies suggest that albumin has adequate binding capacity for the low plasma levels of VLCFA with 20 to 26 carbons, but the protein may not be able to bind longer chain VLCFA.     

Variations in abundance: genome-wide responses to genetic variation and vice versa

How do naturally occurring polymorphisms in DNA sequence relate to variation in gene expression? Recent work to map genetic sources of expression variation has shown a surprising balance between cis and trans effects. Other work suggests some chromosomal clustering of genes by expression pattern. A synthesis of approaches may provide new insight in to adaptive mechanisms in evolution and the population basis of complex traits.     

Plants versus animals: do they deal with stress in different ways?

Both plants and animals respond to stress by using adaptationsthat help them evade, tolerate, or recover from stress. In asynthetic paper A. D. Bradshaw (1972) noted that basic biologicaldifferences between plants and animals will have diverse evolutionaryconsequences, including those influencing how they deal withstress. For instance, Bradshaw argued that animals, becausethey have relatively well-developed sensory and locomotor capacities,can often use behavior and movement to evade or ameliorate environmentalstresses. In contrast, he predicted that plants will have toemphasize increased physiological tolerance or phenotypic plasticity,and also that plants should suffer stronger selection and showmore marked differentiation along environmental gradients. Herewe briefly review the importance of behavior in mitigating stress,the behavioral capacities of animals and plants, and examplesof plant responses that are functionally similar to behaviorsof animals. Next, we try to test some of Bradshaw's predictions.Unfortunately, critical data often proved non-comparable: plantand animal biologists often study different stressors (e.g.,water versus heat) and measure different traits (photosynthesisversus locomotion). Nevertheless, we were able to test someof Bradshaw's predictions and some related ones of our own.As Bradshaw predicted, the phenology of plants is more responsiveto climate shifts than is that of animals and the micro-distributionsof non-mobile, intertidal invertebrates ("plant" equivalents)are more sensitive to temperature than are those of mobile invertebrates.However, mortality selection is actually weaker for plants thanfor animals. We hope that our review not only redraws attentionto some fascinating issues Bradshaw raised, but also encouragesadditional tests of his predictions. Such tests should be informative.     

Preliminary characterisation of DML1, an essential Saccharomyces cerevisiae gene related to misato of Drosophila melanogaster

A genetic and cell-biological analysis is provided for Saccharomyces cerevisiae DML1 (YMR211w) encoding a Drosophila melanogaster Misato-like protein. Misato and Dml1p are descendants of an ancestral tubulin-like protein, and exhibit regions with similarity to members of a GTPase family that include eukaryotic tubulin and prokaryotic FtsZ. Deletion of DML1 was lethal to haploid cells; sporulated DML1/dml1Delta heterozygotes from different genetic backgrounds gave rise to no more than two viable spores per tetrad. DAPI staining for DNA in combination with Southern analysis using the mitochondrial genes COX3, 15S_rRNA_2, and COB revealed that a significant portion of the surviving meiotic progeny were [rho(0)] lacking mtDNA. In addition, meiotic transmission of centromeric plasmids also appeared to be impaired. Self-complementation using extra-chromosomal copies of DML1 efficiently restored meiotic inheritance of mtDNA, but improved spore viability ratios only in part. Inheritance of mtDNA could also be restored using misato cDNA. Unscheduled expression of DML1 tethered to the inducible ADH2 promoter altered both mitochondrial dispersion and general cell morphology. We propose that Dml1p and Misato have been co-opted into a role in mtDNA inheritance in yeast, and into a cell division-related mechanism in flies, respectively. Dml1p might additionally function in the partitioning of the mitochondrial organelle itself, or in the segregation of chromosomes, thereby explaining its essential requirement.     

Enhanced muscle glucose uptake facilitates nitrogen efflux from exercised muscle

The hypothesis that glucose ingestion inthe postexercise state enhances the synthesis of glutamine and alaninein the skeletal muscle was tested. Glucose was infused intraduodenallyfor 150 min (44.5 µmol · kg¹ · min¹)beginning 30 min after a 150-min period of exercise(n = 7) or an equivalent durationsedentary period (n = 10) in18-h-fasted dogs. Prior exercise caused a twofold greater increase inlimb glucose uptake during the intraduodenal glucose infusion compared with uptake in sedentary dogs. Arterial glutamine levels fell graduallywith the glucose load in both groups. Net hindlimb glutamine effluxincreased in response to intraduodenal glucose in exercised but notsedentary dogs (P < 0.05-0.01).Arterial alanine levels, depleted by 50% with exercise, rose withintraduodenal glucose in exercised but not sedentary dogs(P < 0.05-0.01). Net hindlimb alanine efflux also rose in exercised dogs in response to intraduodenal glucose (P < 0.05-0.01),whereas it was not different from baseline in sedentary controls forthe first 90 min of glucose infusion. Beyond this point,it, too, rose significantly. We conclude that oral glucosemay facilitate recovery of muscle from prolonged exercise by enhancingthe removal of nitrogen in the form of glutamine andalanine.

     

Factors affecting ammonium uptake in streams – an inter-biome perspective

1. The Lotic Intersite Nitrogen eXperiment (LINX) was a coordinated study of the relationships between North American biomes and factors governing ammonium uptake in streams. Our objective was to relate inter‐biome variability of ammonium uptake to physical, chemical and biological processes. 2. Data were collected from 11 streams ranging from arctic to tropical and from desert to rainforest. Measurements at each site included physical, hydraulic and chemical characteristics, biological parameters, whole‐stream metabolism and ammonium uptake. Ammonium uptake was measured by injection of ¹⁵N‐ammonium and downstream measurements of ¹⁵N‐ammonium concentration. 3. We found no general, statistically significant relationships that explained the variability in ammonium uptake among sites. However, this approach does not account for the multiple mechanisms of ammonium uptake in streams. When we estimated biological demand for inorganic nitrogen based on our measurements of in‐stream metabolism, we found good correspondence between calculated nitrogen demand and measured assimilative nitrogen uptake. 4. Nitrogen uptake varied little among sites, reflecting metabolic compensation in streams in a variety of distinctly different biomes (autotrophic production is high where allochthonous inputs are relatively low and vice versa). 5. Both autotrophic and heterotrophic metabolism require nitrogen and these biotic processes dominate inorganic nitrogen retention in streams. Factors that affect the relative balance of autotrophic and heterotrophic metabolism indirectly control inorganic nitrogen uptake.