β-甘露聚糖酶理化性质与其最适pH的相关性

为了探究影响GH5家族β-甘露聚糖酶最适pH的各种因素,利用该酶的序列信息,构建了基于氨基酸组成的β-甘露聚糖酶理化性质与其最适pH的相关性模型。结果表明:该酶N端氨基酸序列是影响其最适pH的重要因素,在243个理化性质中有17个呈极显著相关,其中7个呈正相关。优化的转移能量参数相关性最高,为0.78:7个正相关的理化性质中,与螺旋相关的理化性质占3个。优化的转移能量参数和螺旋是影响pH稳定性的最重要的因素。所建立的模型为研究该酶酸碱适应性机理提供了一种简单有效的方法。     

Tubulin Double Helix: Lateral and Longitudinal Curvature Changes of Tubulin Protofilament

By virtue of their native structures, tubulin dimers are protein building blocks that are naturally preprogrammed to assemble into microtubules (MTs), which are cytoskeletal polymers. Here, polycation‐directed (i.e., electrostatically tunable) assembly of tubulins is demonstrated by conformational changes to the tubulin protofilament in longitudinal and lateral directions, creating tubulin double helices and various tubular architectures. Synchrotron small‐angle X‐ray scattering and transmission electron microscopy reveal a remarkable range of nanoscale assembly structures: single‐ and double‐layered double‐helix tubulin tubules. The phase transitions from MTs to the new assemblies are dependent on the size and concentration of polycations. Two characteristic scales that determine the number of observed phases are the size of polycation compared to the size of tubulin (≈4 nm) and to MT diameter (≈25 nm). This work suggests the feasibility of using polycations that have scissor‐ and glue‐like properties to achieve “programmable breakdown” of protein nanotubes, tearing MTs into double‐stranded tubulins and building up previously undiscovered nanostructures. Importantly, a new role of tubulins is defined as 2D shape‐controllable building blocks for supramolecular architectures. These findings provide insight into the design of protein‐based functional materials, for example, as metallization templates for nanoscale electronic devices, molecular screws, and drug delivery vehicles.     

Reversible Quadruple Switching with Optical,Chiroptical, Helicity,and Macropattern in Self‐Assembled Spiropyran Gels

Enantiomeric glutamate gelators containing a spiropyran moiety are designed and found to self‐assemble into a nanohelix through gelation. Upon alternating UV and visible light irradiation, the spiropyran experiences a reversible change between a blue zwitterionic merocyanine state and a colorless closed ring state spiropyran in supramolecular gels. This photochromic switch causes a series of subsequent changes in the optical, chiroptical, morphological properties from supramolecular to macroscopic levels. While the solution of the gelator molecules does not show any circular dichroism (CD) signal in the region of 250–700 nm due to the fact that the chromophore is far from the chiral center, the gel shows chiroptical signals such as CD and circularly polarized luminescence (CPL) because of the chirality transfer by the self‐assembly. These signals are reversible upon alternating UV/vis irradiation. Therefore, a quadruple optical and chiroptical switch is developed successfully. During such process, the self‐assembled nanostructures from the enantiomeric supramolecular gels also undergo a reversible change between helices and fibers under the alternating UV and visible light trigger. Furthermore, a rewritable material fabricated from their xerogels on a glass is developed. Such rewritable material can be efficiently printed over 30 cycles without significant loss in contrast and resolution using UV and visible light.     

The uracil permease of Schizosaccharomyces pombe: A representative of a family of 10 transmembrane helix transporter proteins of yeasts

The uracil permease gene of Schizosaccharomyces pombe was cloned and sequenced. The deduced protein sequence shares strong similarities with five open reading frames from Saccharomyces cerevisiae, namely the uracil permease encoded by the FUR4 gene, the allantoin permease encoded by DAL4, a putative uridine permease (YBL042C) and two unknown ORFs YOR071c and YLR237w. A topological model retaining ten transmembrane helices, based on predictions and on experimental data established for the uracil permease of S. cerevisiae by Galan and coworkers (1996), is discussed for the four closest proteins of this family of transporters. The sequence of the uracil permease gene of S. pombe has been deposited in the EMBL data bank under Accession Number X98696. © 1998 John Wiley & Sons, Ltd.     

γ-(S)-Guanidinylmethyl-Modified Triplex-Forming Peptide Nucleic Acids Increase Hoogsteen-Face Affinity for a MicroRNA and Enhance Cellular Uptake

γ-Modified (i.e., (S)-aminomethyl, (S)-acetamidomethyl, (R)-4-(hydroxymethyl)triazol-1-ylmethyl, and (S)-guanidinylmethyl) triplex-forming peptide nucleic acids (TFPNAs) were synthesized and the effect of the backbone modifications on the binding to a miR-215 model was studied. Among the modifications, an appropriate pattern of three γ-(S)-guanidinylmethyl modifications increased the affinity and Hoogsteen-face selectivity for the miR-215 model without ternary (PNA)₂/RNA complex formation. Moreover, the γ-(S)-guanidinylmethyl groups were observed to facilitate internalization of the TFPNAs into living PC-3 prostate cancer cells.     

Enzymatic activities of Ura2 and Ura1 proteins (aspartate carbamoyltransferase and dihydro-orotate dehydrogenase) are present in both isolated membranes and cytoplasm of Saccharomyces cerevisiae

Computational analysis predicted three potential hydrophobic transmembrane alpha-helices within the Ura2 multidomain protein of Saccharomyces cerevisiae, the C-terminal subdomain of which catalyses the second step of uridine-monophosphate biosynthesis by its L-aspartate carbamoyltransferase activity (EC 2.1.3.2). The fourth step of pyrimidine biosynthesis is catalysed by dihydro-orotate dehydrogenase (Ura1 protein; EC 1.3.99.11), which was similarly characterized as a peripheral membrane protein. Ex situ, the activities of the investigated enzymes were associated both with isolated yeast membranes, fractionated by differential centrifugation to remove intact nuclei, and with soluble cytoplasmic proteins.     

Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction

The structural features of helical transmembrane (TM) proteins, such as helical kinks, tilts, and rotational orientations are important in modulation of their function and these structural features give rise to functional diversity in membrane proteins with similar topology. In particular, the helical kinks caused by breaking of the backbone hydrogen bonds lead to hinge bending flexibility in these helices. Therefore it is important to understand the nature of the helical kinks and to be able to reproduce these kinks in structural models of membrane proteins. We have analyzed the position and extent of helical kinks in the transmembrane helices of all the crystal structures of membrane proteins taken from the MPtopo database, which are about 405 individual helices of length between 19 and 35 residues. 44% of the crystal structures of TM helices showed a significant helical kink, and 35% of these kinks are caused by prolines. Many of the non-proline helical kinks are caused by other residues like Ser and Gly that are located at the center of helical kinks. The side chain of Ser makes a hydrogen bond with the main chain carbonyl of the i − 4th or i + 4th residue thus making a kink. We have also studied how well molecular dynamics (MD) simulations on isolated helices can reproduce the position of the helical kinks in TM helices. Such a method is useful for structure prediction of membrane proteins. We performed MD simulations, starting from a canonical helix for the 405 TM helices. 1 ns of MD simulation results show that we can reproduce about 79% of the proline kinks, only 59% of the vestigial proline kinks and 18% of the non-proline helical kinks. We found that similar results can be obtained from choosing the lowest potential energy structure from the MD simulation. 4–14% more of the vestigial prolines were reproduced by replacing them with prolines before performing MD simulations, and changing the amino acid back to proline after the MD simulations. From these results we conclude that the position of the helical kinks is dependent on the TM sequence. However the extent of helical kinking may depend on the packing of the rest of the protein and the lipid bilayer.