Viral ion channels: structure and function

Viral ion channels are short auxiliary membrane proteins with a length of ca. 100 amino acids. They are found in enveloped viruses from influenza A, influenza B and influenza C (Orthomyxoviridae), and the human immunodeficiency virus type 1 (HIV-1, Retroviridae). The channels are called M2 (influenza A), NB (influenza B), CM2 (influenza C) and Vpu (HIV-1). Recently, in Paramecium bursaria chlorella virus (PBCV-1, Phycodnaviridae), a K+ selective ion channel has been discovered. The viral channels form homo oligomers to allow an ion flux and represent miniaturised systems. Proton conductivity of M2 is established; NB, Vpu and the potassium channel from PBC-1 conduct ions; for CM2 ion conductivity is still under proof. This review summarises the current knowledge of these short viral membrane proteins. Their discovery is outlined and experimental evidence for their structure and function is discussed. Studies using computational methods are presented as well as investigations of drug-protein interactions.     

A historical biophysical dogma vs. an understanding of the structure and function of voltage-gated tetrameric ion channels. A review

The outstanding work of several eminent biophysicists has allowed the functional features of voltage-gated tetrameric ion channels to be disclosed using ingenious and sophisticated electrophysiological techniques. However, the kinetics and mechanism underlying these functions have been heavily conditioned by an arbitrary interpretation of the groundbreaking results obtained by Hodgkin and Huxley (HH) in their investigation of sodium and potassium currents using the voltage clamp technique. Thus, the heavy parametrization of their results was considered to indicate that any proposed sequence of closed states terminates with a single open state. This ‘dogma’ of HH parametrization has influenced the formulation of countless mechanistic models, mainly stochastic, requiring a high number of free parameters and of often unspecified conformational states. This note aims to point out the advantages of a deterministic kinetic model that simulates the main features of tetrameric ion channels using only two free parameters by assuming their stepwise opening accompanied by a progressively increasing cation flow. This model exploits the electrostatic attractive interactions stemming from the charge distribution shared by all tetrameric ion channels, providing a close connection between their structure and function. Quite significantly, a stepwise opening of all ligand-gated tetrameric ion channels, such as glutamate receptors (GluRs), with concomitant ion flow, is nowadays generally accepted, not having been influenced by this dogma. This provides a unified picture of both voltage-gated and ligand-gated tetrameric ion channels.     

The structure and function of glutamate receptor ion channels

As in the case of many ligand-gated ion channels, the biochemical and electrophysiological properties of the ionotropic glutamate receptors have been studied extensively. Nevertheless, we still do not understand the molecular mechanisms that harness the free energy of agonist binding, first to drive channel opening, and then to allow the channel to close (desensitize) even though agonist remains bound. Recent crystallographic analyses of the ligand-binding domains of these receptors have identified conformational changes associated with agonist binding, yielding a working hypothesis of channel function. This opens the way to determining how the domains and subunits are assembled into an oligomeric channel, how the domains are connected, how the channel is formed, and where it is located relative to the ligand-binding domains, all of which govern the processes of channel activation and desensitization.     

L-type voltage-gated calcium channels: understanding function through structure

L-type voltage-gated calcium channels (VGCCs) are multisubunit membrane proteins that regulate calcium influx into excitable cells. Within the last two years there have been four separate reports describing the structure of the skeletal muscle VGCC determined by electron microscopy and single particle analysis methods. There are some discrepancies between the structures, as well as reports for both monomeric and dimeric forms of the channel. This article considers each of the VGCC structures in terms of similarities and differences with an emphasis upon translation of data into a biological context.     

Phylogeny of ion channels: clues to structure and function

Voltage-gated ion channels are responsible for the electrical activity in a variety of cell types in modern-day animals. However, they represent the result of many millions of years of evolution of a family of ion channel proteins that are also found in prokaryotes and diverse eukaryotes, and probably exist in all life forms. This review traces the evolution of ion channels, with particular emphasis on the factors and evolutionary pathways that may have given rise to voltage-gated potassium (K+), calcium (Ca2+), and sodium (Na+) channels. The review also highlights the utility of comparing phylogenetically distinct versions of the same protein as a means to better understand the structure and function of proteins.     

Toward an understanding of the physiological function of Mammalian stem cells

Stem cell biology has the potential to yield new therapies, new insights into disease, and a clearer understanding of tissue formation and maintenance. However, much of what we know about many stem cells is based upon experiments performed in culture. Stem cells sometimes exhibit critical differences in their properties or regulation between the culture and in vivo environments. Though cell lines with stem cell properties can be derived from the long-term culture of diverse tissues, it is not clear whether cells with similar properties exist in vivo. If the goal is to use differentiated cells for therapy or drug screening, it may not matter whether these stem cells exist in vivo. However, to understand tissue development/maintenance or the role of stem cells in disease, it is important to characterize progenitor function in vivo to evaluate physiological significance.     

The structure of TRPC ion channels

Briefly review the recent structural work of transient receptor potential canonical (TRPC) ion channels by using electron cryo-microscopy (cryo-EM). The high resolution structures of TRPC3, TRPC4, TRPC5 and TRPC6 are discussed.     

Toward understanding the structure and interactions of microtubules and motor proteins

To obtain an overall three-dimensional picture of the interaction between microtubules and the motor proteins of the kinesin family it will be necessary to take account of both atomic resolution structures obtained by X-ray crystallography and medium resolution reconstructions obtained by electron cryomicroscopy. We examine the problems associated with obtaining the required structural information from electron micrographs of vitreous ice-embedded microtubules decorated with motor domains. We find that the minus-end directed motor, ncd, decorates microtubules with an 80 Å periodicity as for kinesin. Our theoretical analysis and experiments with ncd illustrate the difficulty in determining unambiguously the surface lattice organization by diffraction analysis of micrographs. 3D reconstructions of decorated microtubules are required to accurately locate the motor domains. Helical diffraction theory is not usually applicable because microtubules are cylindrical structures that rarely have complete helical symmetry. We propose using a back-projection method based on the long pitch helices formed by individual protofilaments. Model reconstructions show that this approach is feasible. © 1995 Wiley-Liss, Inc.     

The structure and regulation of magnesium selective ion channels

The magnesium ion (Mg^2 +) is the most abundant divalent cation within cells. In man, Mg^2 +-deficiency is associated with diseases affecting the heart, muscle, bone, immune, and nervous systems. Despite its impact on human health, little is known about the molecular mechanisms that regulate magnesium transport and storage. Complete structural information on eukaryotic Mg^2 +-transport proteins is currently lacking due to associated technical challenges. The prokaryotic MgtE and CorA magnesium transport systems have recently succumbed to structure determination by X-ray crystallography, providing first views of these ubiquitous and essential Mg^2 +-channels. MgtE and CorA are unique among known membrane protein structures, each revealing a novel protein fold containing distinct arrangements of ten transmembrane-spanning α-helices. Structural and functional analyses have established that Mg^2 +-selectivity in MgtE and CorA occurs through distinct mechanisms. Conserved acidic side-chains appear to form the selectivity filter in MgtE, whereas conserved asparagines coordinate hydrated Mg^2 +-ions within the selectivity filter of CorA. Common structural themes have also emerged whereby MgtE and CorA sense and respond to physiologically relevant, intracellular Mg^2 +-levels through dedicated regulatory domains. Within these domains, multiple primary and secondary Mg^2 +-binding sites serve to staple these ion channels into their respective closed conformations, implying that Mg^2 +-transport is well guarded and very tightly regulated. The MgtE and CorA proteins represent valuable structural templates to better understand the related eukaryotic SLC41 and Mrs2–Alr1 magnesium channels. Herein, we review the structure, function and regulation of MgtE and CorA and consider these unique proteins within the expanding universe of ion channel and transporter structural biology.     

The construction of an amino acid network for understanding protein structure and function

Amino acid networks (AANs) are undirected networks consisting of amino acid residues and their interactions in three-dimensional protein structures. The analysis of AANs provides novel insight into protein science, and several common amino acid network properties have revealed diverse classes of proteins. In this review, we first summarize methods for the construction and characterization of AANs. We then compare software tools for the construction and analysis of AANs. Finally, we review the application of AANs for understanding protein structure and function, including the identification of functional residues, the prediction of protein folding, analyzing protein stability and protein–protein interactions, and for understanding communication within and between proteins.     

Differential regulation of ion channels function by proteolysis

Ion channels are pore-forming protein complexes in membranes that play essential roles in a diverse array of biological activities. Ion channel activity is strictly regulated at multiple levels and by numerous cellular events to selectively activate downstream effectors involved in specific biological activities. For example, ions, binding proteins, nucleotides, phosphorylation, the redox state, channel subunit composition have all been shown to regulate channel activity and subsequently allow channels to participate in distinct cellular events. While these forms of modulation are well documented and have been extensively reviewed, in this article, we will first review and summarize channel proteolysis as a novel and quite widespread mechanism for altering channel activity. We will then highlight the recent findings demonstrating that proteolysis profoundly alters Inositol 1,4,5 trisphosphate receptor activity, and then discuss its potential functional ramifications in various developmental and pathological conditions.     

Toward an understanding of the structural basis of translation

The recently solved X-ray crystal structures of the ribosome have provided opportunities for studying the molecular basis of translation with a variety of methods including cryo-electron microscopy - where maps give the first glimpses of ribosomal evolution - and fluorescence spectroscopy techniques.