Crystallographic Analyses of Ion Channels: Lessons and Challenges

Membrane proteins fascinate at many levels, from their central functional roles in transport, energy transduction, and signal transduction processes to structural questions concerning how they fold and operate in the exotic environments of the membrane bilayer and the water-bilayer interface and to methodological issues associated with studying membrane proteins either in situ or extracted from the membrane. This interplay is beautifully exemplified by ion channels, a collection of integral membrane proteins that mediate the transmembrane passage of ions down their electrochemical potential gradient (for general reviews, see Refs. 1 and 2). Ion channels are key elements of signaling and sensing pathways, including nerve cell conduction, hormone response, and mechanosensation. The characteristic properties of ion channels reflect their conductance, ion selectivity, and gating. Ion channels are often specific for a particular type of ion (such as potassium or chloride) or a class of ions (such as anions) and are typically regulated by conformational switching of the protein structure between "open" and "closed" states. This conformational switching may be gated in response to changes in membrane potential, ligand binding, or application of mechanical forces. Detailed functional characterizations of channels and their gating mechanisms have been achieved, reflecting exquisite methodological advances such as patch clamp methods that can monitor the activities of individual channels (3). Until recently, corresponding information about the three-dimensional structures of channels was not available, reflecting difficulties in obtaining sufficient quantities of membrane proteins for crystallization trials. Happily, this situation has started to change with the structure determinations of the Streptomyces lividans K+ channel (KcsA (4)) and the Mycobacterium tuberculosis mechanosensitive channel (MscL (5)). A variety of reviews (6-12) have appeared recently that discuss functional implications of these channel structures. This review discusses these developments from a complementary perspective, by considering the implications of these structures from within the larger framework of membrane protein structure and function. Because of space restrictions, this review necessarily emphasizes membrane proteins that are composed primarily of alpha-helical bundles, such as KcsA and MscL, rather than beta-barrel proteins, such as porins, typically found in bacterial outer membranes

The Lyman Break Galaxies: their Progenitors and Descendants

We study the evolution of Lyman Break Galaxies (LBGs) from z=5 to z=0 by tracing the merger trees of galaxies in a large-scale hydrodynamic simulation based on a Lambda cold dark matter model. In particular, we emphasize on the range of properties of the sample selected by the rest-frame V band luminosity, in accordance with recent near-IR observations. The predicted rest-frame V band luminosity function agrees well with the observed one when dust extinction is taken into account. The stellar content and the star formation histories of LBGs are also studied. We find that the LBGs intrinsically brighter than Mv=-21.0 at z=3 have stellar masses of at least 10^9\Msun, with a median of 10^{10}h^{-1}\Msun. The brightest LBGs (Mv<-23) at z=3 merge into clusters/groups of galaxies at z=0, as suggested from clustering studies of LBGs. Roughly one half of the galaxies with -23<Mv<-22 at z=3 fall into groups/clusters, and the other half become typical L* galaxies at z=0 with stellar mass of ~10^{11}\Msun. Descendants of LBGs at the present epoch have formed roughly 30% of their stellar mass by z=3, and the half of their current stellar population is 10 Gyr old, favoring the scenario that LBGs are the precursors of the present day spheroids. We find that the most luminous LBGs have experienced a starburst within 500 Myr prior to z=3, but also have formed stars continuously over a period of 1 Gyr prior to z=3 when all the star formation in progenitors is coadded. We also study the evolution of the mean stellar metallicity distribution of galaxies, and find that the entire distribution shifts to lower metallicity at higher redshift. The observed sub-solar metallicity of LBGs at z=3 is naturally predicted in our simulation.Comment: 29 pages, including 11 figures, ApJ in press. One reference adde

The Bacterial Photosynthetic Reaction Center as a Model for Membrane Proteins

Membrane proteins participate in many fundamental cellular processes. Until recently, an understanding of the function and properties of membrane proteins was hampered by an absence of structural information at the atomic level. A landmark achievement toward understanding the structure of membrane proteins was the crystallization (1) and structure determination (2-5) the photosynthetic reaction center (RC) from the purple bacteria Rhodopseudomonas viridis, followed by that of the RC from Rhodobacter sphaeroides (6-17). The RC is an integral membrane protein-pigment complex, which carries out the initial steps of photosynthesis (reviewed in 18). RCs from the purple bacteria Rps. viridis and Rb. sphaeroides are composed of three membrane-associated protein subunits (designated L, M, and H), and the following cofactors: four bacteriochlorophylls (Bchl or B), two bacteriopheophytins (Bphe or [phi]), two quinones, and a nonheme iron. The cofactors are organized into two symmetrical branches that are approximately related by a twofold rotation axis (2, 8). A central feature of the structural organization of the RC is the presence of 11 hydrophobic [alpha]-helixes, approximately 20-30 residues long, which are believed to represent the membrane-spanning portion of the RC (3, 9). Five membrane-spanning helixes are present in both the L and M subunits, while a single helix is in the H subunit. The folding of the L and M subunits is similar, consistent with significant sequence similarity between the two chains (19-25). The L and M subunits are approximately related by the same twofold rotation axis that relates the two cofactor branches. RCs are the first membrane proteins to be described at atomic resolution; consequently they provide an important model for discussing the folding of membrane proteins. The structure demonstrates that [alpha]-helical structures may be adopted by integral membrane proteins, and provides confirmation of the utility of hydropathy plots in identifying nonpolar membrane-spanning regions from sequence data. An important distinction between the folding environments of water-soluble proteins and membrane proteins is the large difference in water concentration surrounding the proteins. As a result, hydrophobic interactions (26) play very different roles in stabilizing the tertiary structures of these two classes of proteins; this has important structural consequences. There is a striking difference in surface polarity of membrane and water-soluble proteins. However, the characteristic atomic packing and surface area appear quite similar. A computational method is described for defining the position of the RC in the membrane (10). After localization of the RC structure in the membrane, surface residues in contact with the lipid bilayer were identified. As has been found for soluble globular proteins, surface residues are less well conserved in homologous membrane proteins than the buried, interior residues. Methods based on the variability of residues between homologous proteins are described (13); they are useful (a) in defining surface helical regions of membrane and water-soluble proteins and (b) in assigning the side of these helixes that are exposed to the solvent. A unifying view of protein structure suggests that water-soluble proteins may be considered as modified membrane proteins with covalently attached polar groups that solubilize the proteins in aqueous solution

Spectra of Unsteady Wind Models of Gamma-Ray Bursts

We calculate the spectra expected from unsteady relativistic wind models of gamma-ray bursts, suitable for events of arbitrary duration. The spectral energy distribution of the burst is calculated over photon energies spanning from eV to TeV, for a range of event durations and variability timescales. The relative strength of the emission at different wavelengths can provide valuable information on the particle acceleration, radiation mechanisms and the possible types of models.Comment: 10 pages, 2 postscript figures included, uses aaspp4.sty. Accepted for publication in the Astrophysical Journal Letters. Also available at http://www.astro.psu.edu/users/hara/Preprints/xxx_sub.p

Can explicit training in Cued Speech improve phoneme identification?

When identifying phonemes in new spoken words, lipreading is an important source of information for many deaf people. Because many groups of phonemes are virtually indistinguishable by sight, deaf people are able to identify about 30% of phonemes when lipreading non-words. Cued speech (CS) is a system of hand shapes and hand positions used alongside speech to disambiguate similarities in lip patterns. Deaf children exposed to CS from under 3 years of age go on to develop age-appropriate language and literacy skills. However, there are no studies evaluating the explicit training of CS with older deaf children. This study is the first part of a long-term project to develop and evaluate a computer-delivered programme to teach school-aged deaf children to recognize cued phonemes. Sixty-two adult hearing participants were allocated to a single training session in one of three training conditions: cued speech training (CST), lipreading training and auditory training in noise. They were all tested on their ability to identify 13 phonemes in non-words when denied access to sound. The CST group made highly significant improvements in identifying cued phonemes and these changes could not be explained by lipreading practice or familiarization with a closed set of phonemes. Improvements generalized to non-words that were not used in training. This suggests that explicit training in CS could help deaf children to identify cued phonemes in new words. Practical implications of introducing the teaching of CS to selected deaf children are discussed

A Model for the Moving `Wisps' in the Crab Nebula

I propose that the moving `wisps' near the center of the Crab Nebula result from nonlinear Kelvin-Helmholtz instabilities in the equatorial plane of the shocked pulsar wind. Recent observations suggest that the wisps trace out circular wavefronts in this plane, expanding radially at speeds approximately less than c/3. Instabilities could develop if there is sufficient velocity shear between a faster-moving equatorial zone and a slower moving shocked pulsar wind at higher latitudes. The development of shear could be related to the existence of a neutral sheet -- with weak magnetic field -- in the equatorial zone, and could also be related to a recent suggestion by Begelman that the magnetic field in the Crab pulsar wind is much stronger than had been thought. I show that plausible conditions could lead to the growth of instabilities at the radii and speeds observed, and that their nonlinear development could lead to the appearance of sharp wisplike features.Comment: 7 pages; 3 postscript figures; LaTex, uses emulateapj.sty; to Appear in the Astrophysical Journal, Feb. 20, 1999, Vol. 51

Afterglow Light Curve Modulated by a Highly Magnetized Millisecond Pulsar

We investigate consequences of a continuously energy-injecting central engine of gamma-ray burst (GRB) afterglow emission, assuming that a highly magnetized pulsar is left beaming in the core of a GRB progenitor. Beaming and continuous energy-injection are natural consequences of the pulsar origin of GRB afterglows. Whereas previous studies have considered continuous energy-injection from a new-born pulsar to interpret the deviation of afterglow light curves of GRBs from those with the simple power law behavior, a beaming effect, which is one of the most important aspects of pulsar emissions, is ignored in earlier investigations. We explicitly include the beaming effect and consider a change of the beaming with time due to a dynamical evolution of a new-born pulsar. We show that the magnitude of the afterglow from this fireball indeed first decreases with time, subsequently rises, and declines again. One of the most peculiar optical afterglows light curve of GRB 970508 can be accounted for by continuous energy injection with beaming due to a highly magnetized new-born pulsar. We discuss implications on such observational evidence for a pulsar.Comment: 4 pages, 1 table, submitted to Astronomy and Astrophysics (Letters