Solitons and energy transfer along protein molecules

It is shown that the energy released in the hydrolysis of ATP molecules can be transferred in the form of vibration solitons along α-helical protein molecules. The vibration solitons are collective excitations travelling along a chain of successively arranged peptide groups and corresponding to amide I vibrations. The exceptional stability of solitons in one-dimensional structures can account for the small probability of their energy transforming into that of disordered heat motion.     

Lateral proton conduction at a lipid/water interface. Effect of lipid nature and ionic content of the aqueous phase

Fast lateral proton conduction was observed along the lipid/water interface using a fluorescence technique. This conduction can be detected for a large number of lipids, both phospholipids and glycolipids. The efficiency of the proton transfer is dependent on the molecular packing of the host lipid at a given surface pressure. The proton conduction which is present in the liquid expanded state is abolished by the transition to the liquid condensed state. The proton transfer is affected slightly by the ionic content of the aqueous subphase except in the case of calcium which can inhibit the conduction along phosphatidylglyceroethanolamine. We suggest that the transfer of the protons occurs along a bidimensional hydrogen-bond network formed from the polar head groups, their water molecules of hydration and the water molecules which are intercalated between the lipid molecules.     

Migration of neuronal cells along the anterior-posterior body axis of C. elegans: Wnts are in control

Migrating neuronal cells are directed to their final positions by an array of guidance cues. It has been shown that guidance molecules such as UNC-6/Netrin and SLT-1/Slit play a major role in controlling cell and axon migrations along the dorsal-ventral body axis. Much less is known, however, about the mechanisms that mediate migration along the anterior-posterior (AP) body axis. Recent research in Caenorhabditis elegans has uncovered an important role of the Wnt family of signalling molecules in controlling AP-directed neuronal cell migration and polarity. A common theme that emerges from these studies is that multiple Wnt proteins function in parallel as instructive cues or permissive signals to control neuronal patterning along this major body axis.     

Brownian dynamics simulation of knot diffusion along a stretched DNA molecule

Manipulation of individual DNA molecules by optical tweezers has made it possible to tie these molecules into knots. After stretching the DNA molecules the knots become highly localized. In their recent study, Quake and co-authors investigated diffusion of such knots along stretched DNA molecules. We used these data to test the accuracy of a Brownian dynamics simulation of DNA bending motion. We simulated stretched DNA molecules with knots 3(1), 4(1), and 7(1), and determined their diffusion coefficients. Comparison of the simulated and experimental results shows that Brownian dynamics simulation is capable of predicting the rates of large-scale DNA rearrangements within a factor of 2.     

Molecular packing and intermolecular interactions in two structural polymorphs of N-palmitoylethanolamine, a type 2 cannabinoid receptor agonist

The molecular structure, packing properties, and intermolecular interactions of two structural polymorphs of N-palmitoylethanolamine (NPEA) have been determined by single-crystal X-ray diffraction. Polymorphs alpha and beta crystallized in monoclinic space group P2(1)/c and orthorhombic space group Pbca, respectively. In both polymorphs, NPEA molecules are organized in a tail-to-tail manner, resembling a bilayer membrane. Although the molecular packing in polymorph alpha is similar to that in N-myristoylethanolamine and N-stearoylethanolamine, polymorph beta is a new form. The acyl chains in both polymorphs are tilted by approximately 35 degrees with respect to the bilayer normal, with their hydrocarbon moieties packed in an orthorhombic subcell. In both structures, the hydroxy group of NPEA forms two hydrogen bonds with the hydroxy groups of molecules in the opposite leaflet, resulting in extended, zig-zag type H-bonded networks along the b-axis in polymorph alpha and along the a-axis in polymorph beta. Additionally, the amide N-H and carbonyl groups of adjacent molecules are involved in N-H...O hydrogen bonds that connect adjacent molecules along the b-axis and a-axis, respectively, in alpha and beta. Whereas in polymorph alpha the L-shaped NPEA molecules in opposite layers are arranged to yield a Z-like organization, in polymorph beta one of the two NPEA molecules is rotated 180 degrees , leading to a W-like arrangement. Lattice energy calculations indicate that polymorph alpha is more stable than polymorph beta by approximately 2.65 kcal/mol.     

Differing cell surface distribution of human leukocyte antigen-DR molecules on epidermal Langerhans cells and eccrine duct cells.

Scanning electron microscopy (SEM) with immunogold labeling was employed to observe the undersurface of the human epidermis after it was split from dermal connective tissue, in an attempt to localize the molecules actually expressed on cell/tissue surfaces. We found that human leukocyte antigen-DR (HLA-DR) molecules were expressed on the surfaces of eccrine duct cells as well as those of epidermal Langerhans cells (LC) in normal skin. HLA-DR molecules, visualized by the deposition of gold particles, were distributed evenly on the LC surface but were present only along the interdigitating borders of the individual duct cells, thus producing a meshwork pattern on the duct surface. Transmission electron microscopy confirmed that the gold particles labeling cell surface HLA-DR molecules were seen only on the portions of duct cell membranes the interdigitated with neighboring duct cells. These findings suggest that the function of HLA-DR molecules may vary with their location and distribution. On the LC surface, the evenly distributed molecules seem to be well suited for promoting "accessory cell" functions. On duct cell surfaces, the HLA-DR molecules present along the intercellular spaces may be involved in trapping various peptide antigens that pass into the sweat gland filtrate and then are reabsorbed by the excretory duct, since these molecules have a highly permissive capacity for binding various peptides.     

Expression and function of cell adhesion molecules during neural crest migration

Neural crest cells are highly migratory cells that give rise to many derivatives including peripheral ganglia, craniofacial structures and melanocytes. Neural crest cells migrate along defined pathways to their target sites, interacting with each other and their environment as they migrate. Cell adhesion molecules are critical during this process. In this review we discuss the expression and function of cell adhesion molecules during the process of neural crest migration, in particular cadherins, integrins, members of the immunoglobulin superfamily of cell adhesion molecules, and the proteolytic enzymes that cleave these cell adhesion molecules. The expression and function of these cell adhesion molecules and proteases are compared across neural crest emigrating from different axial levels, and across different species of vertebrates.     

Protein structure and import into the peroxisomal matrix

Proteins destined for the peroxisomal matrix are synthesized in the cytosol, and imported post-translationally. It has been previously demonstrated that stably folded proteins are substrates for peroxisomal import. Mammalian peroxisomes do not contain endogenous chaperone molecules. Therefore, it is possible that proteins are required to fold into their stable, tertiary conformation in order to be imported into the peroxisome. These investigations were undertaken to determine whether proteins rendered incapable of folding were also substrates for import into peroxisomes. Reduction of albumin resulted in a less compact tertiary structure as measured by analytical centrifugation. Microinjection of unfolded albumin molecules bearing the PTS1 targeting signal resulted in their import into peroxisomes. Kinetic analysis indicated that native and unfolded molecules were imported into peroxisomes at comparable rates. While import was unaffected by treatment with cycloheximide, hsc70 molecules were observed to be imported along with the unfolded albumin molecules. These results indicate that proteins, which are incapable of assuming their native conformation, are substrates for peroxisomal import. When combined with previous observations demonstrating the import of stably folded proteins, these results support the model that tertiary structure has no effect on protein import into the peroxisomal matrix .     

Invariant Sema5A inhibition serves an ensheathing function during optic nerve development

Retinal axon pathfinding from the retina into the optic nerve involves the growth promoting axon guidance molecules L1, laminin and netrin 1, each of which governs axon behavior at specific regions along the retinal pathway. In identifying additional molecules regulating this process during embryonic mouse development, we found that transmembrane Semaphorin5A mRNA and protein was specifically expressed in neuroepithelial cells surrounding retinal axons at the optic disc and along the optic nerve. Given that growth cone responses to a specific guidance molecule can be altered by co-exposure to a second guidance cue, we examined whether retinal axon responses to Sema5A were modulated by other guidance signals axons encountered along the retinal pathway. In growth cone collapse, substratum choice and neurite outgrowth assays, Sema5A triggered an invariant inhibitory response in the context of L1, laminin, or netrin 1 signaling, suggesting that Sema5A inhibited retinal axons throughout their course at the optic disc and nerve. Antibody-perturbation studies in living embryo preparations showed that blocking of Sema5A function led to retinal axons straying out of the optic nerve bundle, indicating that Sema5A normally helped ensheath the retinal pathway. Thus, development of some CNS nerves requires inhibitory sheaths to maintain integrity. Furthermore, this function is accomplished using molecules such as Sema5A that exhibit conserved inhibitory responses in the presence of co-impinging signals from multiple families of guidance molecules.     

Diffusion and directed movement: in vitro motile properties of fission yeast kinesin-14 Pkl1

Fission yeast Pkl1 is a kinesin-14A family member that is known to be localized at the cellular spindle and is capable of hydrolyzing ATP. However, its motility has not been detected. Here, we show that Pkl1 is a slow, minus end-directed microtubule motor with a maximum velocity of 33+/-9 nm/s. The Km,MT value of steady-state ATPase activity of Pkl1 was as low as 6.4+/-1.1 nM, which is 20-30 times smaller than that of kinesin-1 and another kinesin-14A family member, Ncd, indicating a high affinity of Pkl1 for microtubules. However, the duty ratio of 0.05 indicates that Pkl1 spends only a small fraction of the ATPase cycle strongly associated with a microtubule. By using total internal reflection fluorescence microscopy, we demonstrated that single molecules of Pkl1 were not highly processive but only exhibited biased one-dimensional diffusion along microtubules, whereas several molecules of Pkl1, probably fewer than 10 molecules, cooperatively moved along microtubules and substantially reduced the diffusive component in the movement. Our results suggest that Pkl1 molecules work in groups to move and generate forces in a cooperative manner for their mitotic functions.     

Directional motility of kinesin motor proteins

Kinesin motor proteins are molecules capable of moving along microtubules. They share homology in the so-called core motor domain which acts as a microtubule-dependent ATPase. The surprising finding that different members of the superfamily move in opposite directions along microtubules despite their close similarity has stimulated intensive research on the determinants of motor directionality. This article reviews recent biophysical, biochemical, structural and mutagenic studies that contributed to the elucidation of the mechanisms that cause directional motion of kinesin motor proteins.     

Mechanism of processive movement of monomeric and dimeric kinesin molecules

Kinesin molecules are motor proteins capable of moving along microtubule by hydrolyzing ATP. They generally have several forms of construct. This review focuses on two of the most studied forms: monomers such as KIF1A (kinesin-3 family) and dimers such as conventional kinesin (kinesin-1 family), both of which can move processively towards the microtubule plus end. There now exist numerous models that try to explain how the kinesin molecules convert the chemical energy of ATP hydrolysis into the mechanical energy to "power" their processive movement along microtubule. Here, we attempt to present a comprehensive review of these models. We further propose a new hybrid model for the dimeric kinesin by combining the existing models and provide a framework for future studies in this subject.     

MOLPACK: molecular graphics,for studying the packing of protein molecules in the crystallographic unit cell

A graphics program, MOLPACK, has been developed on the Silicon Graphics IRIS-4D computer system for displaying the packing of proteins in the crystallographic unit cell. In addition to the normal viewing operations of rotation, translation and scaling, the program has the ability to translate molecules along the cell axes while maintaining their crystallographic equivalent positions within the unit cell. This allows the user to observe the packing of protein molecules generated by molecular replacement, to create a new packing model or to locate an unknown molecule. A special feature of the program is that up to four independent molecules can be manipulated in the asymmetric unit.     

Origin of the phyla and cancer

Multicelled animals with specialized cells (metazoans) emerged shortly after rising oxygen levels in the seas permitted formation of collagen-family molecules. Certain unicells then formed 3-D clusters, some with disc- or ball-like shapes that happened to resemble blastulas. These became unstable beyond a certain size due to contrasting metabolic styles among their component cells. For whereas cells near their exteriors could employ oxygen respiration, cells closer to the oxygen-deprived interiors were obliged to rely on anaerobic metabolism (fermentation), a process that produces waste molecules that, if retained within cells, cause disproportionate cell growth. Unstable blastula-like forms would either disintegrate or reorganize along surfaces of relative weakness in a process that may be likened to gastrulation. Initial cell-differentiation depended on the quantity and diversity of retained fermentation products and on the pumping of molecules from cell to cell by the consequent electro-chemical gradients. In subsequent contexts, oxygen deprivation, fermentation, excess cell growth, and disintegration or reorganization of tissues produce cancer.     

Crystals of native and modified bovine rhodopsins and their heavy atom derivatives

Rhodopsin, the pigment protein responsible for dim-light vision, is a G protein-coupled receptor that converts light absorption into the activation of a G protein, transducin, to initiate the visual response. We have crystallised detergent-solubilised bovine rhodopsin in the native form and after chemical modifications as needles 10-40 microm in cross-section. The crystals belong to the trigonal space group P3(1), with two molecules of rhodopsin per asymmetric unit, related by a non-crystallographic 2-fold axis parallel with the crystallographic screw axis along c (needle axis). The unit cell dimensions are a=103.8 A, c=76.6 A for native rhodopsin, but vary over a wide range after heavy atom derivatisation, with a between 101.5 A and 113.9 A, and c between 76.6 A and 79.2 A. Rhodopsin molecules are packed with the bundle of transmembrane helices tilted from the c-axis by about 100 degrees . The two molecules in the asymmetric unit form contacts along the entire length of their transmembrane helices 5 in an antiparallel orientation, and they are stacked along the needle axis according to the 3-fold screw symmetry. Hence hydrophobic contacts are prominent at protein interfaces both along and normal to the needle axis. The best crystals of native rhodopsin in this crystal form diffracted X-rays from a microfocused synchrotron source to 2.55 A maximum resolution. We describe steps taken to extend the diffraction limit from about 10 A to 2.6 A.     

Building a synapse: lessons on synaptic specificity and presynaptic assembly from the nematode C. elegans

Synapses are specialized sites of cell contact that mediate information flow between neurons and their targets. Genetic screens in the nematode C. elegans have led to the discovery of a number of molecules required for synapse patterning and assembly. Recent studies have demonstrated the importance of guidepost cells in the positioning of presynaptic sites at specific locations along the axon. Interestingly, these guideposts can promote or inhibit synapse formation, and do so by utilizing transmembrane adhesion molecules or secreted factors that act over relatively larger distances. Once the decision of where to build a presynaptic terminal has been made, key molecules are recruited to assemble synaptic vesicles and active zone proteins at that site. Multiple steps of this process are regulated by ubiquitin ligase complexes. Interestingly, some of the molecules involved in presynaptic assembly also play roles in regulating axon polarity and outgrowth, suggesting that different neurodevelopmental processes are molecularly integrated.     

Supramolecular organization of double-stranded DNA molecules in the columnar hexagonal liquid crystalline phase. An electron microscopic analysis using freeze-fracture methods

I present an electron microscopical analysis of the columnar hexagonal liquid crystalline phase of DNA. Freeze-fracture methods reveal that this phase is a lamellar structure, each layer (30 to 40 A thick) composed of DNA molecules aligned in parallel. Numerous defects can be seen in the structure, and their nature is determined. I show that they are mainly screw dislocations of both handedness. By this method it is possible to follow individual double-stranded DNA molecules in this highly packed structure. I show, moreover, that there is a local twist between DNA molecules along the screw dislocation lines and that this twist can be either right-handed or left-handed. The interest of such ultrastructural analysis is discussed in relation to the understanding of chromatin structure.     

晶态下氯化氨甲酰胆碱结构研究

应用X衍射分析确定了晶态下氯化氨甲酰胆碱分子的结构,它们形成以氢键联结的沿晶胞c方向延伸的两个互为对映、相间分布的螺旋型多聚体结构。     

Molecular packing and intermolecular interactions in N-acylethanolamines: crystal structure of N-myristoylethanolamine.

N-Acylethanolamines elicited much interest in recent years owing to their occurrence in biological membranes under conditions of stress as well as under normal conditions. The molecular conformation, packing properties and intermolecular interactions of N-myristoylethanolamine (NMEA) have been determined by single crystal X-ray diffraction analysis. The lipid crystallized in the space group P21/a with unit cell dimensions: a=9.001, b=4.8761, c=39. 080. There are four symmetry-related molecules in the monoclinic unit cell. The molecules are organized in a tail-to-tail fashion, similar to the arrangement in a bilayer membrane. The hydrophobic acyl chain of the NMEA molecule is tilted with respect to the bilayer normal by an angle of 37 degrees. Each hydroxy group forms two hydrogen bonds, one as a donor and the other as an acceptor, with the hydroxy groups of molecules in the opposing leaflet. These O-H...O hydrogen bonds form an extended, zig-zag type network along the b-axis. In addition, the N-H and C=O groups of adjacent molecules are involved in N-H...O hydrogen bonds, which also connect adjacent molecules along the b-axis.