Permeation of ions across the potassium channel: brownian dynamics studies

The physical mechanisms underlying the transport of ions across a model potassium channel are described. The shape of the model channel corresponds closely to that deduced from crystallography. From electrostatic calculations, we show that an ion permeating the channel, in the absence of any residual charges, encounters an insurmountable energy barrier arising from induced surface charges. Carbonyl groups along the selectivity filter, helix dipoles near the oval chamber, and mouth dipoles near the channel entrances together transform the energy barrier into a deep energy well. Two ions are attracted to this well, and their presence in the channel permits ions to diffuse across it under the influence of an electric field. Using Brownian dynamics simulations, we determine the magnitude of currents flowing across the channel under various conditions. The conductance increases with increasing dipole strength and reaches its maximum rapidly; a further increase in dipole strength causes a steady decrease in the channel conductance. The current also decreases systematically when the effective dielectric constant of the channel is lowered. The conductance with the optimal choice of dipoles reproduces the experimental value when the dielectric constant of the channel is assumed to be 60. The current-voltage relationship obtained with symmetrical solutions is linear when the applied potential is less than approximately 100 mV but deviates from Ohm's law at a higher applied potential. The reversal potentials obtained with asymmetrical solutions are in agreement with those predicted by the Nernst equation. The conductance exhibits the saturation property observed experimentally. We discuss the implications of these findings for the transport of ions across the potassium channels and membrane channels in general.     

The mouse alpha-amylase multigene family. Sequence organization of members expressed in the pancreas, salivary gland and liver

The DNAs that specify the α-amylase messenger RNAs found in the pancreas, salivary gland and liver of mouse strain A have been isolated by molecular cloning in phage λ. Amylase clones were studied by mRNA/DNA hybrid analysis in the electron microscope, restriction endonuclease site mapping and DNA sequencing. The Amy-2^a gene, which specifies pancreatic α-amylase mRNA, measures 10·1 kb from cap to polyadenylation site and is interrupted by at least 9 intervening sequences. Amy-1^a, which specifies both salivary gland and liver α-amylase mRNAs contains at least 10 introns. The distance between the cap and polyadenylation sites used in the salivary gland and the liver measures 22·9 kb and 20 kb, respectively. Introns are located at very similar, if not identical, positions within comparable regions of Amy-1^a and Amy-2^a. The first intron of Amy-1^a, which interrupts sequences specifying 5′ non-translated regions of salivary gland and liver α-amylase mRNAs, has no counterpart in Amy-2^a. Some introns exhibit considerable sequence homology, suggesting that Amy-1^a and Amy-2^a have evolved by duplication from a common split ancestor sequence. Repetitive sequence elements occur in the introns and flanking regions of these genes. Gene titration by quantitative autoradiography reveals only one copy of Amy-1^a, but two copies of Amy-2^a per haploid mouse genome. In addition to Amy-1^a and Amy-2^a, several other amylase-like DNA sequences exist in the mouse genome. No gross rearrangements of amylase DNA sequences can be detected between germline DNA and that of various mouse tissues.     

Morphology, histochemistry, and function of epaxial cervical musculature in the horse (Equus caballus).

The semispinalis capitis and splenius muscles of the horse were analyzed for gross morphology, microarchitecture, fiber length, and fiber type. Although these two muscles are similar in size and anatomical position, they are very different from one another in structural design and histochemistry, implying diverse functional roles in the animal's behavior. The histochemical staining profile was limited to two fiber types: slow oxidative and fast glycolytic. The splenius muscle has simple architecture, long fibers, and a 60/40 ratio of SO to FG cross-sectional area. The semispinalis capitis has complex architecture with short-fibered, concentric compartments dorsal to its central tendon and longer-fibered compartments ventrally. The entire dorsal region has an increasing gradient of slow oxidative fiber percentage from caudal to cranial (58-71% SO). In contrast, the ventral region has a decreasing gradient of slow oxidative fibers from caudal to cranial (48-67% FG). These patterns can be interpreted within the context of the cervical musculature during locomotion and posture to indicate the functional advantages of this organization.     

Thermodynamic stability of beta-peptide helices and the role of cyclic residues

Beta-peptides are emerging as an attractive class of peptidomimetic molecules. In contrast to naturally occurring alpha-peptides, short oligomers of beta-amino acids (comprising just 4-6 monomers) exhibit stable secondary structures that make them amenable for quantitative, concerted experimental and theoretical studies of the effects of particular chemical interactions on structure. In this work, molecular simulations are used to study the thermodynamic stability of helical conformations formed by beta-peptides containing varying proportions of acyclic (beta(3)) and cyclic (ACH) residues. More specifically, several beta-peptides differing only in their content of cyclic residues are considered in this work. Previous computational studies of beta-peptides have relied mostly on energy minimization of molecular dynamics simulations. In contrast, our study relies on density-of-states based Monte Carlo simulations to calculate the free energy and examine the stability of various folded structures of these molecules along a well-defined order parameter. By resorting to an expanded-ensemble formalism, we are able to determine the free energy required to unfold specific molecules, a quantity that could be measured directly through single-molecule force spectroscopy. Simulations in both implicit and explicit solvents have permitted a systematic study of the role of cyclic residues and electrostatics on the stability of secondary structures. The molecules considered in this work are shown to exhibit stable H-14 helical conformations and, in some cases, relatively stable H-12 conformations, thereby suggesting that solvent quality may be used to manipulate the hydrogen-bonding patterns and structure of these peptides.     

Mechanical stability of helical beta-peptides and a comparison of explicit and implicit solvent models

Synthetic β-peptide oligomers have been shown to form stable folded structures analogous to those encountered in naturally occurring proteins. Literature studies have speculated that the conformational stability of β-peptides is greater than that of α-peptides. Direct measurements of that stability, however, are not available. Molecular simulations are used in this work to quantify the mechanical stability of four helical β-peptides. This is achieved by subjecting the molecules to tension. The potential of mean force associated with the resulting unfolding process is determined using both an implicit and an explicit solvent model. It is found that all four molecules exhibit a highly stable helical structure. It is also found that the energetic contributions to the potential of mean force do not change appreciably when the molecules are stretched in explicit water. In contrast, the entropic contributions decrease significantly. As the peptides unfold, a loss of intramolecular energy is compensated by the formation of additional water-peptide hydrogen bonds. These entropic effects lead in some cases to a loss of stability upon cooling the peptides, a phenomenon akin to the cold denaturing of some proteins. While the location of the free energy minimum and the structural helicity of the peptides are comparable in the implicit-solvent and explicit-water cases, it is found that, in general, the helical structure of the molecules is more stable in the implicit solvent model than in explicit water.     

Rex1/Zfp42 is dispensable for pluripotency in mouse ES cells

Background  

Rex1/Zfp42 has been extensively used as a marker for the undifferentiated state of pluripotent stem cells. However, its function in pluripotent stem cells including embryonic stem (ES) cells remained unclear although its involvement in visceral endoderm differentiation in F9 embryonal carcinoma (EC) cells was reported.     

Bacterial species selective toxicity of two isomeric alpha/beta-peptides: role of membrane lipids

We have studied how membrane interactions of two synthetic cationic antimicrobial peptides with alternating alpha- and beta-amino acid residues ("alpha/beta-peptides") impact toxicity to different prokaryotes. Electron microscopic examination of thin sections of Escherichia coli and of Bacillus subtilis exposed to these two alpha/beta-peptides reveals different structural changes in the membranes of these bacteria. These two peptides also have very different effects on the morphology of liposomes composed of phosphatidylethanolamine and phosphatidylglycerol in a 2:1 molar ratio. Freeze fracture electron microscopy indicates that with this lipid mixture, alpha/beta-peptide I induces the formation of a sponge phase. 31P NMR and X-ray diffraction are consistent with this conclusion. In contrast, with alpha/beta-peptide II and this same lipid mixture, a lamellar phase is maintained, but with a drastically reduced d-spacing. alpha/beta-Peptide II is more lytic to liposomes composed of these lipids than is I. These findings are consistent with the greater toxicity of alpha/beta-peptide II, relative to alpha/beta-peptide I, to E. coli, a bacterium having a high content of phosphatidylethanolamine. In contrast, both alpha/beta-peptides display similar toxicity toward B. subtilis, in accord with the greater anionic lipid composition in its membrane. This work shows that variations in the selectivity of these peptidic antimicrobial peptides toward different strains of bacteria can be partly determined by the lipid composition of the bacterial cell membrane.