Apolipoprotein E structure: insights into function

Human apolipoprotein E (apoE) is a member of the family of soluble apolipoproteins. Through its interaction with members of the low-density lipoprotein receptor family, apoE has a key role in lipid transport both in the plasma and in the central nervous system. Its three common structural isoforms differentially affect the risk of developing atherosclerosis and neurodegenerative disorders, including Alzheimer's disease. Because the function of apoE is dictated by its structure, understanding the structural properties of apoE and its isoforms is required both to determine its role in disease and for the development of therapeutic strategies.     

The PLD superfamily: insights into catalysis

Knowledge of the PLD superfamily is rapidly expanding and new insights into the mechanism and regulation of the superfamily are rapidly emerging. The recent structural analysis and use of mutant proteins suggest a mechanism that involves two active sites acting in concert. While a number of residues are required for activity, it appears most likely that a histidine is the residue that becomes covalently linked to phosphatidate in catalysis. Evidence for these proposals is covered in this article.     

The PLD superfamily: insights into catalysis.

Knowledge of the PLD superfamily is rapidly expanding and new insights into the mechanism and regulation of the superfamily are rapidly emerging. The recent structural analysis and use of mutant proteins suggest a mechanism that involves two active sites acting in concert. While a number of residues are required for activity, it appears most likely that a histidine is the residue that becomes covalently linked to phosphatidate in catalysis. Evidence for these proposals is covered in this article.     

Prokaryotic Kdp-ATPase: recent insights into the structure and function of KdpB

P-type ATPases are amongst the most abundant enzymes that are responsible for active transport of ions across biological membranes. Within the last 5 years a detailed picture of the structure and function of these transport ATPases has emerged. Here, we report on the recent progress in elucidating the molecular mechanism of a unique, prokaryotic member of P-type ATPases, the Kdp-ATPase. The review focuses on the catalytic parts of the central subunit, KdpB. The structure of the nucleotide-binding domain was solved by NMR spectroscopy at high resolution and a model of the nucleotide-binding mode was presented. The nucleotide turned out to be 'clipped' into the binding pocket by a pi-pi interaction to F377 on one side and a cation-pi interaction to K395 on the other. The 395KGXXD/E motif and thus the nucleotide-binding mode seems to be conserved in all P-type ATPases, except the heavy metal-transporting (class IB) ATPases. Hence, it can be concluded that KdpB is currently misgrouped as class IA. Mutational studies on two highly conserved residues (D583 and K586) in the transmembrane helix 5 of KdpB revealed that they are indispensable in coupling ATP hydrolysis to ion translocation. Based on these results, two possible pathways for the reaction cycle are discussed.     

New insights into pectin methylesterase structure and function

In bacteria, fungi and plants, pectin methylesterases are ubiquitous enzymes that modify the degree of methylesterification of pectins, which are major components of plant cell walls. Such changes in pectin structure are associated with changes in cellular adhesion, plasticity, pH and ionic contents of the cell wall and influence plant development and stress responses. In plants, pectin methylesterases belong to large multigene families, are regulated in a highly specific manner, and are involved in vegetative and reproductive processes, including wood and pollen formation, in addition to plant-pathogen interactions. Although, overall, protein structures are highly conserved between isoforms, recent data indicate that structural variations might be associated with the targeting and functions of specific pectin methylesterases.     

Intrinsic disorder in the kinesin superfamily

Kinesin molecular motors perform a myriad of intracellular transport functions. While their mechanochemical mechanisms are well understood and well-conserved throughout the superfamily, the cargo-binding and regulatory mechanisms governing the activity of kinesins are highly diverse and, in general, incompletely characterized. Here we present evidence from bioinformatic predictions indicating that most kinesin superfamily members contain significant regions of intrinsically disordered (ID) residues. ID regions can bind to multiple partners with high specificity and are highly labile to post-translational modification and degradation signals. In kinesins, the predicted ID regions are primarily found in areas outside the motor domains, where primary sequences diverge by family, suggesting that the ID may be a critical structural element for determining the functional specificity of individual kinesins. To support this concept, we present a systematic analysis of the kinesin superfamily, family by family, for predicted ID regions. We combine this analysis with a comprehensive review of kinesin-binding partners and post-translational modifications. We find two key trends across the entire kinesin superfamily. First, ID residues tend to be in the tail regions of kinesins, opposite the superfamily-conserved motor domains. Second, predicted ID regions correlate to regions that are known to bind to cargoes and/or undergo post-translational modifications. We therefore propose that the ID residue is a structural element utilized by the kinesin superfamily in order to impart functional specificity to individual kinesins.     

New molecular insights into CETP structure and function: a review

Cholesteryl ester transfer protein (CETP) is important clinically and is the current target for new drug development. Its structure and mechanism of action has not been well understood. We have combined current new structural and functional methods to compare with relevant prior data. These analyses have led us to propose several steps in CETP's function at the molecular level, in the context of its interactions with lipoproteins, e.g., sensing, penetration, docking, selectivity, ternary complex formation, lipid transfer, and HDL dissociation. These new molecular insights improve our understanding of CETP's mechanisms of action.     

New insights into the structure and function of potassium channels.

Potassium channels are surprisingly modular proteins. Well-defined regions that determine functional properties such as ion conduction and gating have recently been identified.     

The kinesin superfamily: tails of functional redundancy

Kinesin is a microtubule-based motility protein that mediates axonal transport and perhaps other intracellular movements in eukaryotic cells. Recent research has indicated that the principal component of kinesin, the kinesin heavy chain, is but one member of an extended superfamily of kinesin-like microtubule motor proteins. These proteins appear to have diverse microtubule-based motility functions--in mitosis, meiosis, vesicle transport and organelle transport. The various kinesin-like molecules may play overlapping or redundant roles in these processes.     

The surprising proton channel: Novel insights into its structure and function

Commentary to: Tombola F, Ulbrich M, Isacoff I. The voltage-gated proton channel Hv1 has two pores, each controlled by one voltage sensor. Neuron 2008; 58:546-66.

Commentary to: Lee S-Y, Letts JA, MacKinnon R. Dimeric subunit stoichiometry of the human voltage-dependent proton channel Hv1. Proc Natl Acad Sci 2008; 105:7692-5.     

Adaptation of proximal tubular structure and function: insights into compensatory renal hypertrophy

Hypertrophy of the renal tubular cells, especially those of the proximal tubule (PT), accounts for the majority of the increase in kidney size that follows partial removal of renal mass. The propensity of PTs to enlarge appears to be closely linked to an elevation in glomerular filtration rate and may be related to altered tubular fluid flow rate. Hypertrophied PTs reabsorb fluid at an increased rate in vitro, which indicates an intrinsic adaptation of their transport capacity. The hypertrophied cells demonstrate a predominant increase in basolateral membrane area with little change in luminal surface area. This asymmetric structural hypertrophy does not, however, appear to be accompanied by functional asymmetry, for basolateral Na+-K+ pump activity increases roughly in proportion to the increase in cell protein. The activity of the Na+-H+ antiporter, on the other hand, is increased in the brush-border membrane of proximal tubules derived from animals with reduced renal mass. In view of the reported association of Na+-H+ antiport stimulation and mitogenesis in a variety of cell types, the increased activity of this transporter, possibly induced by an increase in tubular fluid flow rate, could be the local stimulus that initiates hypertrophy and determines the organ specificity of the response.     

Recent insights into the structure and function of the ribonucleoprotein enzyme ribonuclease P

In bacteria, the tRNA-processing endonuclease ribonuclease P is composed of a large ( approximately 400 nucleotide) catalytic RNA and a smaller ( approximately 100 amino acid) protein subunit that is essential for substrate recognition. Current biochemical and biophysical investigations are providing fresh insights into the modular architecture of the ribozyme, the mechanisms of substrate specificity and the role of essential metal ions in catalysis. Together with recent high-resolution structures of portions of the ribozyme, these findings are beginning to reveal how the functions of RNA and protein are coordinated in this ribonucleoprotein enzyme.