Ju Mei,†,‡,∥ Nelson L. C. Leung,†,‡,∥ Ryan T. K. Kwok,†,‡ Jacky W. Y. Lam,†,‡ and Ben Zhong Tang*,†,‡,§ †HKUST-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China ‡Department of Chemistry, HKUST Jockey Club Institute for Advanced Study, Institute of Molecular Functional Materials, Division of Biomedical Engineering, State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China Guangdong Innovative Research Team, SCUT-HKUST Joint Research Laboratory, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China

Aggregation-Induced Emission: Together We Shine, United We Soar!

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.

http://kinemage.biochem.duke.edu/teaching/workshop/MolProbity/pdfs/2007DavisNAR35.pdf

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

Antibiotic-resistant bacteria that are difficult or impossible to treat are becoming increasingly common and are causing a global health crisis. Antibiotic resistance is encoded by several genes, many of which can transfer between bacteria. New resistance mechanisms are constantly being described, and new genes and vectors of transmission are identified on a regular basis. This article reviews recent advances in our understanding of the mechanisms by which bacteria are either intrinsically resistant or acquire resistance to antibiotics, including the prevention of access to drug targets, changes in the structure and protection of antibiotic targets and the direct modification or inactivation of antibiotics.

Molecular mechanisms of antibiotic resistance.

The bacteria cell envelope is a complex multilayered structure that serves to protect these organisms from their unpredictable and often hostile environment. The cell envelopes of most bacteria fall into one of two major groups. Gram-negative bacteria are surrounded by a thin peptidoglycan cell wall, which itself is surrounded byan outer membrane containing lipopolysaccharide. Gram-positive bacteria lack an outer membrane but are surrounded by layers of peptidoglycan many times thicker than is found in the Gram-negatives. Threading through these layers of peptidoglycan are long anionic polymers, called teichoic acids. The composition and organization of these envelope layers and recent insights into the mechanisms of cell envelope assembly are discussed.

/pdf/the-bacterial-cell-envelope-o3k9u4ycci.pdf

The Bacterial Cell Envelope

The Rho GTPases form a subgroup of the Ras superfamily of 20- to 30-kD GTP-binding proteins that have been shown to regulate a wide spectrum of cellular functions. These proteins are ubiquitously expressed across the species, from yeast to man. The mammalian Rho-like GTPases comprise at least 10 distinct proteins: RhoA, B, C, D, and E; Rac1 and 2; RacE; Cdc42Hs, and TC10. A comparison of the amino acid sequences of the Rho proteins from various species has revealed that they are conserved in primary structure and are 50%–55% homologous to each other. Like all members of the Ras superfamily, the Rho GTPases function as molecular switches, cycling between an inactive GDP-bound state and an active GTP-bound state. Until recently, members of the Rho subfamily were believed to be involved primarily in the regulation of cytoskeletal organization in response to extracellular growth factors. However, research from a number of laboratories over the past few years has revealed that the Rho GTPases play crucial roles in diverse cellular events such as membrane trafficking, transcriptional regulation, cell growth control, and development. Consequently, a major challenge has been to unravel the underlying molecular mechanisms by which the Rho GTPases mediate these various activities. Many targets of the Rho GTPases have now been identified and further characterization of some of them has provided major insights toward our understanding of Rho GTPase function at the molecular level. This review aims to summarize the general established principles about the Rho GTPases and some of the more recent exciting findings, hinting at novel, unanticipated functions of the Rho GTPases.

/pdf/rho-gtpases-and-signaling-networks-48wqq41h57.pdf

Rho GTPases and signaling networks

Lipid–protein interactions as determinants of membrane protein topology

Lipid-protein interactions as a determinant of the function and topogenesis of membrane proteins

Contributors

Publisher Summary This chapter discusses the in vitro synthesis of enzymes involved in membrane biosynthesis in E. coli. Phosphatidyl serine synthase (pss gene locus) catalyzes the committed step in the synthesis of phosphatidylethanolamine in E. coli. This enzyme has been shown to be ribosomal bound in the crude extracts of E. coli, but this association appears to be an artifact of isolation. The properties of the purified enzyme suggest a membrane location for the enzyme in vivo . To study the processes of transcription and translation of the pss gene locus and the subsequent assembly of the gene product into a functional enzyme, the pss gene has been cloned using pBR322 as the cloning vector. The resulting plasmid (pPS4017) directs the synthesis of phosphatidylserine synthase in an E. coli S30 protein synthesizing system.

In vitro synthesis of enzymes involved in membrane biosynthesis in e. coli

A Saccharomyces cerevisiae pgsl null mutant, which is deficient with phosphatidyl glycerol (PG) and cardiolipin (CL) biosynthesis, grows well on most fermentable carbon sources, but fails to grow on non-fermentable carbon sources such as glycerol, ethanol, and lactate. This mutant also cannot grow on galactose medium as the sole carbon source. We found that the incorporation of [ 14 C]-galactose, which is the first step of the galactose metabolic pathway (Leloir pathway), into the pgsl null mutant cell was extremely repressed. Exogenously expressed PGS1 (YCpPGS1) under indigenous promoter could completely restore the pgsl growth defect on non-fermentable carbon sources, and dramatically recovered [ 14 C]-galactose incorporation into the pgs1 mutant cell. However, PGS1 expression under the GAL1 promoter (YEpP GAL1 -PGS1-myc) could not complement pgs1 null mutation, and the GAL2-lacZ fusion gene (YEpP GAL2 -lacZ) also did not exhibit its β-galactosidase activity in the pgsl mutant. In wild-type yeast, antimycin A (1 μg/ml), which inhibits mitochondrial complex III, severely repressed not only the expression of the GAL2-lacZ fusion gene, but also uptake of [ 14 C]-galactose. However, exogenously expressed PGS1 partially relieved these inhibitory effects of antimycin A in both the pgsl mutant and wild-type yeast, although it could not basically restore the growth defect on galactose by antimycin A. These results suggest that the PGS1 gene product has an important role in utilization of galactose by Gal genes, and that intact mitochondrial function with PGS1 should be required for galactose incorporation into the Leloir pathway. The PGS1 gene might provide a clue to resolve the historic issue about the incapability of galactose with deteriorated mitochondrial function.

William Dowhan

Papers

Lipid–protein interactions as determinants of membrane protein topology

Lipid-protein interactions as a determinant of the function and topogenesis of membrane proteins

Contributors

In vitro synthesis of enzymes involved in membrane biosynthesis in e. coli

Incapability of utilizing galactose by pgs1 mutation occurred on the galactose incorporation step in Saccharomyces cerevisiae