Polymorphism of monolayer lipid membrane structures made from unsymmetrical bolaamphiphiles

The crystal structures of synthetic unsymmetrical 1-glucosamide- and 1-galactosamide bolaamphiphiles, 13-[(beta-d-glucopyranosyl)carbamoyl]tridecanoic acid (1) and 15-[(beta-d-galactopyranosyl)carbamoyl]pentadecanoic acid (2), respectively, were elucidated by single-crystal X-ray analysis. The space group for 1 is P2(1), Z=2 with cell dimensions: a=8.6816(9), b=4.8578(5), c=26.250(3)A, beta=91.460(2) degrees ; that for 2P2(1), Z=2 with cell dimensions: a=4.90(1), b=40.139(1), 6.289(1)A, beta=106.48(1) degrees . The glucopyranosyl and galactopyranosyl rings in 1 and 2, respectively, take a (4)C(1) chair conformation. In the crystal lattice, the 1-glucosamide 1 forms a symmetrical monolayer lipid membrane (MLM) structure in which the molecules are packed in an antiparallel fashion, while 1-galactosamide 2 has an unsymmetrical MLM with parallel molecular packing. The stereochemistry of the sugar hydroxy group proved to affect their hydrogen-bonding networks and induce the polymorphism of the MLM.     

Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations

Potassium binding to the 5 S rRNA loop E motif has been studied by molecular dynamics at high (1.0 M) and low (0.2 M) concentration of added KCl in the presence and absence of Mg²⁺. A clear pattern of seven deep groove K⁺ binding sites or regions, in all cases connected with guanine N7/O6 atoms belonging to GpG, GpA, and GpU steps, was identified, indicating that the LE deep groove is significantly more ionophilic than the equivalent groove of regular RNA duplexes. Among all, two symmetry-related sites (with respect to the central G·A pair) were found to accommodate K⁺ ions with particularly long residence times. In a preceding molecular dynamics study by Auffinger et al. in the year 2003, these two sites were described as constituting important Mg²⁺ binding locations. Altogether, the data suggest that these symmetric sites correspond to the loop E main ion binding regions. Indeed, they are located in the deep groove of an important ribosomal protein binding motif associated with a fragile pattern of non-Watson-Crick pairs that has certainly to be stabilized by specific Mg²⁺ ions in order to be efficiently recognized by the protein. Besides, the other sites accommodate monovalent ions in a more diffuse way pointing out their lesser significance for the structure and function of this motif. Ion binding to the shallow groove and backbone atoms was generally found to be of minor importance since, at the low concentration, no well defined binding site could be characterized while high K⁺ concentration promoted mostly unspecific potassium binding to the RNA backbone. In addition, several K⁺ binding sites were located in positions equivalent to water molecules from the first hydration shell of divalent ions in simulations performed with magnesium, indicating that ion binding regions are able to accommodate both mono- and divalent ionic species. Overall, the simulations provide a more precise but, at the same time, a more intricate view of the relations of this motif with its ionic surrounding.     

Structures and target RNA preferences of the RNA-binding protein family of IGF2BPs: An overview

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CTP regulates membrane-binding activity of the nucleoid occlusion protein Noc

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Toward rational protein crystallization: A Web server for the design of crystallizable protein variants

Growing well-diffracting crystals constitutes a serious bottleneck in structural biology. A recently proposed crystallization methodology for "stubborn crystallizers" is to engineer surface sequence variants designed to form intermolecular contacts that could support a crystal lattice. This approach relies on the concept of surface entropy reduction (SER), i.e., the replacement of clusters of flexible, solvent-exposed residues with residues with lower conformational entropy. This strategy minimizes the loss of conformational entropy upon crystallization and renders crystallization thermodynamically favorable. The method has been successfully used to crystallize more than 15 novel proteins, all stubborn crystallizers. But the choice of suitable sites for mutagenesis is not trivial. Herein, we announce a Web server, the surface entropy reduction prediction server (SERp server), designed to identify mutations that may facilitate crystallization. Suggested mutations are predicted based on an algorithm incorporating a conformational entropy profile, a secondary structure prediction, and sequence conservation. Minor considerations include the nature of flanking residues and gaps between mutation candidates. While designed to be used with default values, the server has many user-controlled parameters allowing for considerable flexibility. Within, we discuss (1) the methodology of the server, (2) how to interpret the results, and (3) factors that must be considered when selecting mutations. We also attempt to benchmark the server by comparing the server's predictions with successful SER structures. In most cases, the structure yielding mutations were easily identified by the SERp server. The server can be accessed at http://www.doe-mbi.ucla.edu/Services/SER.     

Synthesis, spectroscopic, structural and electrochemical studies of carboxyl substituted 1,4-naphthoquinones

Two carboxyl substituted quinones and their ethyl esters were prepared by alkylation of 2-methyl-1,4-naphthoquinone (MNQ), also known as menadione or vitamin K₃. All products were characterized by spectroscopic (¹H NMR, ¹³C NMR, IR) and electrochemical (cyclic voltammetry) methods, and the crystal structure of the two carboxylic derivatives was also determined. Both carboxyl substituted quinones crystallize in the system as hydrogen bonded dimers. In MeCN, the cyclic voltammograms of the ester derivatives present two reversible one-electron redox waves very similar to those of the parent quinone, MNQ. However, in the same solvent, the corresponding carboxyl substituted quinones show one cathodic and one anodic additional irreversible waves at more positive potentials and a decrease in current intensity of the two quinone reduction waves accompanied by loss of the quasi-reversible character of the second wave. These results show that the presence of the carboxylic substituent does not greatly modify the redox behaviour of the quinone, except for a small anodic shift of the potentials, but the associated presence of H⁺ ions in solution causes an important perturbation to the system, stabilizing the electrogenerated semiquinones by intermolecular self-protonation and/or hydrogen bonding.     

Generating fibre orientation maps in human heart models using Poisson interpolation

Smoothly varying muscle fibre orientations in the heart are critical to its electrical and mechanical function. From detailed histological studies and diffusion tensor imaging, we now know that fibre orientations in humans vary gradually from approximately ? 70° in the outer wall to +80° in the inner wall. However, the creation of fibre orientation maps for computational analyses remains one of the most challenging problems in cardiac electrophysiology and cardiac mechanics. Here, we show that Poisson interpolation generates smoothly varying vector fields that satisfy a set of user-defined constraints in arbitrary domains. Specifically, we enforce the Poisson interpolation in the weak sense using a standard linear finite element algorithm for scalar-valued second-order boundary value problems and introduce the feature to be interpolated as a global unknown. User-defined constraints are then simply enforced in the strong sense as Dirichlet boundary conditions. We demonstrate that the proposed concept is capable of generating smoothly varying fibre orientations, quickly, efficiently and robustly, both in a generic bi-ventricular model and in a patient-specific human heart. Sensitivity analyses demonstrate that the underlying algorithm is conceptually able to handle both arbitrarily and uniformly distributed user-defined constraints; however, the quality of the interpolation is best for uniformly distributed constraints. We anticipate our algorithm to be immediately transformative to experimental and clinical settings, in which it will allow us to quickly and reliably create smooth interpolations of arbitrary fields from data-sets, which are sparse but uniformly distributed.     

Intracellular ion concentrations and cell volume during cholinergic stimulation of eccrine secretory coil cells

Summary Methacholine (MCh)-induced changes in intracellular concentrations of Na, K, and Cl ([Na]_i, [K]_i, and [Cl]_i, respectively) and in cellular dry mass (a measure of cell shrinkage) were examined in isolated monkey eccrine sweat secretory coils by electron probe X-ray microanalysis using the peripheral standard method. To further confirm the occurrence of cell shrinkage during MCh stimulation, the change in cell volume of dissociated clear and dark cells were directly determined under a light microscope equipped with differential interference contrast (DIC) optics. X-ray microanalysis revealed a biphasic increase in cellular dry mass in clear cells during continuous MCh stimulation; an initial increase of dry mass to 158% (of control) followed by a plateau at 140%, which correspond to the decrease in cell volume of 37 and 29%, respectively. The latter agrees with the MCh-induced cell shrinkage of 29% in dissociated clear cells. The MCh-induced increase in dry mass in myoepithelial cells was less than half that of clear cells. During the steady state of MCh stimulation, both [K]_i and [Cl]_i of clear cells decreased by about 45%, whereas [Na]_i increased in such a way as to maintain the sum of [Na]_i+[K]_i constant. There was a small (12–15mm) increse in [Na]_i and a decrease in [K]_i in myoepithelial cells during stimulation with MCh. Dissociated dark cells failed to significantly shrink during MCh stimulation. The decrease in [Cl]_i in the face of constant [Na]_i+[K]_i suggests the accumulation of unknown anion(s) inside the clear cell during MCh stimulation. While the decrease in [K]_i and [Cl]_i may be instrumental in facilitating influx of ions via Na–K–2Cl cotransporters, the functional significance of MCh-induced cell shrinkage remains unknown.