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

Regulation of phosphatidylglycerophosphate synthase levels in Saccharomyces cerevisiae

Membrane lipids play critical roles in the structure and function of membrane-embedded transporters. Salmonella typhimurium MelB (MelBSt) is a symporter coupling melibiose translocation with a cation (Na+, Li+, or H+). We present an extensive study on the effects of specific phospholipids on the structure of MelBSt and the melibiose transport catalyzed by this protein. Lipidomic analysis and thin-layer chromatography (TLC) experiments reveal that at least one phosphatidylethanolamine (PE) and one phosphatidylglycerol (PG) molecule associate with MelBSt at high affinities. Solid-state nuclear magnetic resonance (ssNMR) spectroscopy experiments confirmed the presence of lipid tails and glycerol backbones that co-purified with MelBSt; headgroups of PG were also observed. Studies with lipid-engineered strains, including PE-deficient, cardiolipin (CL)- and PG-deficient, or CL-deficient strains, show that lack of PE or PG, however not CL, largely inhibits both H+- and Na+-coupled melibiose active transport to different extents. Interestingly, neither the co-substrate binding (melibiose or Na+) nor MelBSt folding and stability are affected by changing lipid compositions. Remarkably, the delipidated MelBSt with only 2–3 bound lipids, regardless of the headgroup species, also exhibits unchanged melting temperature values as shown by circular dichroism spectroscopy. (1) Lipid tails and glycerol backbones of interacting PE and PG may contribute to the stability of the structure of MelBSt. (2) The headgroups of PE and PG, but not of CL, play important roles in melibiose transport; however, lipid headgroups do not modulate the folding and stability of MelBSt.

/pdf/structural-and-functional-characterization-of-protein-lipid-1rpubbs3qg.pdf

Structural and functional characterization of protein-lipid interactions of the Salmonella typhimurium melibiose transporter MelB.

Synthesis of the high-affinity K+-translocating Kdp-ATPase of Escherichia coli, encoded by the kdpFABC operon, is regulated by the membrane-bound sensor kinase KdpD and the soluble response regulator KdpE. K+ limitation or a sudden increase in osmolarity induces the expression of kdpFABC. Due to the importance of K+ to maintain turgor, it has been proposed that KdpD is a turgor sensor. Although the primary stimulus that KdpD senses is unknown, alterations in membrane strain or the interaction between KdpD and membrane components might be good candidates. Here, we report a study of the influence of the membrane phospholipid composition on the function of KdpD in vivo and in vitro using various E. coli mutants defective in phospholipid biosynthesis. Surprisingly, neither the lack of the major E. coli phospholipid phosphatidylethanolamine nor the drastic reduction of the phosphatidylglycerol/cardiolipin content influenced induction of kdpFABC expression significantly. However, in vitro reconstitution experiments with synthetic phospholipids clearly demonstrated that KdpD kinase activity is dependent on negatively charged phospholipids, whereas the structure of the phospholipids plays a minor role. These results indicate that electrostatic interactions are important for the activity of KdpD.

Negatively charged phospholipids influence the activity of the sensor kinase KdpD of Escherichia coli.

Biological membranes define the outer limits of cells and organelles and are composed of phospholipids, glycolipids, sphingolipids, sterols and proteins. Each lipid class is composed of numerous variants within their respective polar and apolar domains. The apolar and polar nature of these amphipathic lipids is the basis for forming biological membranes with which membrane proteins associate either as integral proteins that span the membrane bilayer or as peripheral proteins that associate with the membrane surface. Individual lipids, once thought mainly to provide cell barrier function and a solvent for membrane proteins, are now recognised as critical components that directly influence an array of cellular functions. Physical and chemical properties of lipids that determine the properties of biological membranes, genetic approaches used to alter cellular lipid composition and examples of how lipid–protein interactions define specific roles for lipids in cell function are discussed.

Chapter 1 – Functional Roles of Lipids in Membranes

Publisher Summary Phosphatidylserine decarboxylases have been identified both genetically and biochemically in Escherichia coli (E coli), Saccharomyces, Chinese hamster ovary (CHO) cells, and humans In yeast phosphatidylserine and possibly in all eukaryotic cells there are two nonhomologous decarboxylases In all cases these enzymes are integral membrane proteins requiring the use of detergents for solubilization, purification, and assay The gene encoding each respective decarboxylase has been isolated and sequenced, revealing the sequence of each enzyme The E coli enzyme has been overproduced using a plasmid-borne copy of its gene and purified to homogeneity; the enzyme from rat liver mitochondria has been partially purified The α-amino-acid decarboxylases including mammalian and some bacterial histidine decarboxylases utilize pyridoxal 5'-phosphate as their prosthetic group and in some cases also require pyrroloquinolinequinone This chapter reviews E coli phosphatidylserine decarboxylase and the histidine decarboxylase of Lactobacillus 30a In other well-characterized enzymes of this class, the pyruvoyl residue is covalently bound to the amino terminus of one of the two nonidentical subunits of the E coli phosphatidylserine decarboxylase The enzyme is synthesized as a single subunit proenzyme form, which undergoes posttranslational processing in which an internal serine residue becomes the covalently bound prosthetic group of one of the two resulting subunits

William Dowhan

Papers

Regulation of phosphatidylglycerophosphate synthase levels in Saccharomyces cerevisiae

Structural and functional characterization of protein-lipid interactions of the Salmonella typhimurium melibiose transporter MelB.

Negatively charged phospholipids influence the activity of the sensor kinase KdpD of Escherichia coli.

Chapter 1 – Functional Roles of Lipids in Membranes

Phosphatidylserine decarboxylases: pyruvoyl-dependent enzymes from bacteria to mammals.