The Villin/Gelsolin/Fragmin Superfamily Proteins in Plants

The villin/gelsolin/fragmin superfamily is a conserved Ca^2＋-dependent family of actin-regulating proteins that is widely present both in mammalian and non-mammalian organisms. They have traditionally been characterized by the same core of three or six tandem gelsolin subdomains. The study in vertebrates and lower eukaryotic cells has revealed that the villin/gelsolin/fragmin superfamily of proteins has versatile functions including severing, capping, nucleating or bundling actin filaments. In plants, encouraging progress has been made in this field of research in recent years. This review will summarize the identified plant homologs of villin/gelsolin/fragmin superfamily, thus providing a basis for reflection on their biochemical activities and functions in plants.     

ω-Helices in Proteins

A modification of the α-helix, termed the ω-helix, has four residues in one turn of a helix. We searched the ω-helix in proteins by the HELFIT program which determines the helical parameters—pitch, residues per turn, radius, and handedness—and p = rmsd/(N ? 1)^1/2 estimating helical regularity, where “rmsd” is the root mean square deviation from the best fit helix and “N” is helix length. A total of 1,496 regular α-helices 6–9 residues long with p ≤ 0.10 Å were identified from 866 protein chains. The statistical analysis provides a strong evidence that the frequency distribution of helices versus n indicates the bimodality of typical α-helix and ω-helix. Sixty-two right handed ω-helices identified (7.2% of proteins) show non-planarity of the peptide groups. There is amino acid preference of Asp and Cys. These observations and analyses insist that the ω-helices occur really in proteins.     

Fast and Forceful Refolding of Stretched α-Helical Solenoid Proteins

Anfinsen's thermodynamic hypothesis implies that proteins can encode for stretching through reversible loss of structure. However, large in vitro extensions of proteins that occur through a progressive unfolding of their domains typically dissipate a significant amount of energy, and therefore are not thermodynamically reversible. Some coiled-coil proteins have been found to stretch nearly reversibly, although their extension is typically limited to 2.5 times their folded length. Here, we report investigations on the mechanical properties of individual molecules of ankyrin-R, β-catenin, and clathrin, which are representative examples of over 800 predicted human proteins composed of tightly packed α-helical repeats (termed ANK, ARM, or HEAT repeats, respectively) that form spiral-shaped protein domains. Using atomic force spectroscopy, we find that these polypeptides possess unprecedented stretch ratios on the order of 10-15, exceeding that of other proteins studied so far, and their extension and relaxation occurs with minimal energy dissipation. Their sequence-encoded elasticity is governed by stepwise unfolding of small repeats, which upon relaxation of the stretching force rapidly and forcefully refold, minimizing the hysteresis between the stretching and relaxing parts of the cycle. Thus, we identify a new class of proteins that behave as highly reversible nanosprings that have the potential to function as mechanosensors in cells and as building blocks in springy nanostructures. Our physical view of the protein component of cells as being comprised of predominantly inextensible structural elements under tension may need revision to incorporate springs.     

W-motif Exchange Between β-Propeller Proteins

The similarity between the structural scaffold of PQQGDH and that of sialidase in the absence of any similarity in the primary structure, catalytic function and substrate recognition encouraged us to attempt a W-motif exchange between these enzymes. By substituting one W-motif in PQQGDH with one from sialidase, a chimeric PQQGDH was constructed, and its enzymatic properties were investigated. The overexpression of the chimeric enzyme resulted in the formation of an inclusion body. However, the refolding procedure resulted in a soluble chimeric enzyme with PQQGDH activity showing similar secondary-structure components as native PQQGDH. In contrast to native PQQGDH, the chimeric PQQGDH showed thermal instability and sensitivity to EDTA, ; this difference might have been due to the incomplete compatibility of the inserted W-motif. The potential of W-motif replacement was also discussed in view of the possible molecular evolution/engineering of β-propeller structures.     

Snake Venom C-Type Lectin Related Proteins Up-to-date

The research projects were supported by aresearch scholarship from the National Universityof Singapore,Singapore and by a fund from TheNational Bureau of Foreign Talents,China[2 0 0 1 -1 51 ] .1　 Introduction　　 L ectins are generally considered to be non-enzymatic proteins which selectively bind to spe-cific carbohydrate structure.Animal C- typelectins are a group of proteins which have carbo-hydrate- recognition domains (CRDs) in theirstructures and require calcium ion for their lig-…     

Targeting the Acute Promyelocytic Leukemia-Associated Fusion Proteins PML/RARα and PLZF/RARα with Interfering Peptides

In acute promyelocytic leukemia (APL), hematopoietic differentiation is blocked and immature blasts accumulate in the bone marrow and blood. APL is associated with chromosomal aberrations, including t(15;17) and t(11;17). For these two translocations, the retinoic acid receptor alpha (RARα) is fused to the promyelocytic leukemia (PML) gene or the promyelocytic zinc finger (PLZF) gene, respectively. Both fusion proteins lead to the formation of a high-molecular-weight complex. High-molecular-weight complexes are caused by the “coiled-coil” domain of PML or the BTB/POZ domain of PLZF. PML/RARα without the “coiled-coil” fails to block differentiation and mediates an all-trans retinoic acid-response. Similarly, mutations in the BTB/POZ domain disrupt the high-molecular-weight complex, abolishing the leukemic potential of PLZF/RARα. Specific interfering polypeptides were used to target the oligomerization domain of PML/RARα or PLZF/RARα. PML/RARα and PLZF/RARα were analyzed for the ability to form high-molecular-weight complexes, the protein stability and the potential to induce a leukemic phenotype in the presence of the interfering peptides. Expression of these interfering peptides resulted in a reduced replating efficiency and overcame the differentiation block induced by PML/RARα and PLZF/RARα in murine hematopoietic stem cells. This expression also destabilized the PLZF/RARα-induced high-molecular-weight complex formation and caused the degradation of the fusion protein. Targeting fusion proteins through interfering peptides is a promising approach to further elucidate the biology of leukemia.     

Drosophila Mechanotransduction—Linking Proteins and Functions

The sensation of touch, gravity, and sound all rely on dedicated ion channels that transduce mechanical stimulus forces into electrical response signals. The functional workings and molecular identities of these mechanotransducer channels are little understood. Recent work shows that the mechanotransducers for fly and vertebrate hearing share equivalent gating mechanisms, whereby this mechanism can be probed non-invasively in the mechanics of the Drosophila ear. Here, we describe how this mechanics can be used to evaluate the roles of identified proteins in the process of mechanosensation and, specifically, their contributions to mechanotransduction.     

Nuclear Functions for Plasma Membrane-Associated Proteins?

There are a growing number of observations that proteins, which were initially thought to perform a specific function in a given subcellular compartment, may also play additional roles in different locations within the cell. Proteins found in adhesion and endocytic structures of the plasma membrane and which also traffic to the nucleus perhaps represent the more spectacular examples of this phenomenon. The mechanisms involved in the transport of these molecules through the nuclear pores and their potential nuclear functions are discussed.     

The Effect of Loops on the Structural Organization of α-Helical Membrane Proteins

Loops connecting the transmembrane (TM) α-helices in membrane proteins are expected to affect the structural organization of the thereby connected helices and the helical bundles as a whole. This effect, which has been largely ignored previously, is studied here by analyzing the x-ray structures of 41 α-helical membrane proteins. First we define the loop flexibility ratio, R, and find that 53% of the loops are stretched, where a stretched loop constrains the distance between the two connected helices. The significance of this constraining effect is supported by experiments carried out with bacteriorhodopsin and rhodopsin, in which cutting or eliminating their (predominately stretched) loops has led to a decrease in protein stability, and for rhodopsin, in most cases, also to the destruction of the structure. We show that for nonstretched loops in the extramembranous regions, the fraction of hydrophobic residues is comparable to that for soluble proteins; furthermore (as is also the case for soluble proteins), the hydrophobic residues in these regions are preferentially buried. This is expected to lead to the compact structural organization of the loops, which is transferred to the TM helices, causing them to assemble. We argue that a soluble protein complexed with a membrane protein similarly promotes compactness; other properties of such complexes are also studied. We calculate complementary attractive interactions between helices, including hydrogen bonds and van der Waals interactions of sequential motifs, such as GXXXG. The relative and combined effects of all these factors on the association of the TM helices are discussed and protein structures with only a few of these factors are analyzed. Our study emphasizes the need for classifying membrane proteins into groups according to structural organization. This classification should be considered when procedures for structural analysis or prediction are developed and applied. Detailed analysis of each structure is provided at http://flan.blm.cs.cmu.edu/memloop/     

Rieske Iron–Sulfur Proteins from Extremophilic Organisms

Proteins located on the outside of the membranes of organisms thriving under extreme conditions like high or low pH, or high salinity face special challenges maintaining their structural integrity. This review is focused on the Rieske iron-sulfur proteins from these organisms. Rieske proteins are essential subunits of the cytochrome bc-complexes, which are often of crucial importance for the energy metabolism of the cells. On the basis of the available data we propose strategies by which these proteins are able to stabilize their noncovalent bound cofactor and adapt to the function under extreme conditions.     

Antigenic Properties of Bacteriophage φ29 Structural Proteins

Serological methods and electron microscopy were used to study the structural proteins of the small Bacillus subtilis bacteriophage phi29. This virus has a large number of fibers attached at both ends of its prolate head. A complex neck assembly is comprised of 12 symmetrically arranged appendages as the outer component. Head fibers, neck appendages, and the head surface bind anti-phi29 antibodies. Immune sera absorbed with defective lysates of suppressor-sensitive (sus) mutants have been used to determine the genetic control of neck appendages production. Studies on the serum-blocking power of lysates defective in different tail components showed that appendages contain the main serum-blocking protein. This finding suggests an essential role of the neck appendages in phage adsorption or DNA injection.