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Structures of membrane protein

Seema Qamar, GuoZhen Wang, Suzanne J Randle, Francesco Simone Ruggeri, Juan A Varela, Julie Qiaojin Lin, Emma C Phillips, Akinori Miyashita, Declan Williams, Florian Ströhl, William Meadows, Rodylyn Ferry, Victoria J Dardov, Gian G Tartaglia, Lindsay A Farrer, Gabriele S Kaminski Schierle, Clemens F Kaminski, Christine E Holt, Paul E Fraser, Gerold Schmitt-Ulms, David Klenerman, Tuomas Knowles, Michele Vendruscolo, Peter St George-Hyslop
Reversible phase separation underpins the role of FUS in ribonucleoprotein granules and other membrane-free organelles and is, in part, driven by the intrinsically disordered low-complexity (LC) domain of FUS. Here, we report that cooperative cation-π interactions between tyrosines in the LC domain and arginines in structured C-terminal domains also contribute to phase separation. These interactions are modulated by post-translational arginine methylation, wherein arginine hypomethylation strongly promotes phase separation and gelation...
April 19, 2018: Cell
Takuya Yoshizawa, Rustam Ali, Jenny Jiou, Ho Yee Joyce Fung, Kathleen A Burke, Seung Joong Kim, Yuan Lin, William B Peeples, Daniel Saltzberg, Michael Soniat, Jordan M Baumhardt, Rudolf Oldenbourg, Andrej Sali, Nicolas L Fawzi, Michael K Rosen, Yuh Min Chook
Liquid-liquid phase separation (LLPS) is believed to underlie formation of biomolecular condensates, cellular compartments that concentrate macromolecules without surrounding membranes. Physical mechanisms that control condensate formation/dissolution are poorly understood. The RNA-binding protein fused in sarcoma (FUS) undergoes LLPS in vitro and associates with condensates in cells. We show that the importin karyopherin-β2/transportin-1 inhibits LLPS of FUS. This activity depends on tight binding of karyopherin-β2 to the C-terminal proline-tyrosine nuclear localization signal (PY-NLS) of FUS...
April 19, 2018: Cell
Bercem Dutagaci, Lim Heo, Michael Feig
A refinement protocol based on physics-based techniques established for water soluble proteins is tested for membrane protein structures. Initial structures were generated by homology modeling and sampled via molecular dynamics simulations in explicit lipid bilayer and aqueous solvent systems. Snapshots from the simulations were selected based on scoring with either knowledge-based or implicit membrane-based scoring functions and averaged to obtained refined models. The protocol resulted in consistent and significant refinement of the membrane protein structures similar to the performance of refinement methods for soluble proteins...
April 20, 2018: Proteins
Xiaolin Zhang, Anmin Jiang, Banghua Qi, Hao Yu, Youyi Xiong, Guoliang Zhou, Meisong Qin, Jinfeng Dou, Jianfei Wang
Human neutrophil peptide 1 (HNP1) is a small (3.44 kDa) cationic peptide that is a distinct member of the defensin family. HNP1 plays a crucial role in controlling bacterial infections, particularly by antibiotic-resistant bacteria, through membrane perforation patterns. The structural characteristics of HNP1's three intramolecular disulfide bridges cause difficulty in its synthesis via chemical methods. In this study, bioactive recombinant HNP1 was produced using the Pichia pastoris (P. Pichia) expression system...
April 19, 2018: Applied Microbiology and Biotechnology
Juan Tang, Hao-Yan Yin, Jun-Long Zhang
The Golgi apparatus is well-known as the center of vesicle trafficking whose malfunction might cause the breakdown of overall cellular architecture and ultimately cell death. The development of fluorescent probes to not only precisely stain the Golgi apparatus but also monitor dynamic vesicle trafficking is of great significance. While fluorescent proteins and fluorescent lipid analogs have been reported, they are sometime limited by either overexpression and toxicity or lack of high selectivity, respectively...
February 21, 2018: Chemical Science
Sharon O'Neill, Magalie Mathis, Lidija Kovacic, Suisheng Zhang, Juergen Reinhardt, Dimitri Scholz, Ulrich Schopfer, Rochdi Bouhelal, Ulla G Knaus
Protein-protein interactions critically regulate many biological systems, but quantifying functional assembly of multi-pass membrane complexes in their native context is still challenging. Here, we combined modeling-assisted protein modification and information from human disease variants with a minimal-size fusion tag, split-luciferase-based approach to probe assembly of the NADPH oxidase 4 (NOX4)-p22phox enzyme, an integral membrane complex with unresolved structure, which is required for electron transfer and generation of reactive oxygen species (ROS)...
April 19, 2018: Journal of Biological Chemistry
Sindhoora Bhargavi Gopala Reddy, Wei-Xin Chin, Nanjunda Swamy Shivananju
Despite the ever increasing global incidence of dengue fever, there are no specific chemotherapy regimens for its treatment. Structural studies on dengue virus (DENV) proteins have revealed potential drug targets. Major DENV proteins such as the envelope protein and non-structural (NS) proteins 3 and 5 have been extensively investigated in antiviral studies, but with limited success in vitro. However, the minor NS proteins NS2 and NS4 have remained relatively underreported. Emerging evidence indicating their indispensable roles in virus propagation and host immunomodulation should encourage us to target these proteins for drug discovery...
April 16, 2018: Biochemical Pharmacology
M R Plewes, P D Burns, P E Graham, J E Bruemmer, T E Engle
Biological membranes are composed of a lipid bilayer and proteins that form lipid microdomains. This study examined the effects of fish byproducts on lipid-protein interactions within lipid microdomains of bovine luteal cells. In Exp. 1 and 2, luteal cells were prepared from corpora lutea (CL; n = 4 to 8) collected at an abattoir. Exp. 1 was conducted to optimize ultrasonication in a detergent-free protocol for isolation of lipid microdomains. A power setting of 10 to 20% was effective in isolating lipid microdomains from bulk lipid...
March 31, 2018: Animal Reproduction Science
Yuqing Chong, Huarong Huang, Guiqiong Liu, Xunping Jiang, Weiheng Rong
Zona pellucida 3 (ZP3) is a primary sperm receptor and acrosome reaction inducer. As a candidate gene, the ZP3 gene has been widely studied since it has great influence on reproductive traits in farm animals. However, little is known about the association between polymorphisms of the coding region of the ZP3 gene and the first parity litter size in Hu sheep. Therefore, the objective of this study was to identify single nucleotide polymorphisms (SNPs) of the ZP3 gene associated with the first parity litter size in Hu sheep...
March 31, 2018: Animal Reproduction Science
Kwame Kumi Asare, Miako Sakaguchi, Amuza Byaruhanga Lucky, Masahito Asada, Shinya Miyazaki, Yuko Katakai, Satoru Kawai, Chihong Song, Kazuyoshi Murata, Kazuhide Yahata, Osamu Kaneko
During development within the host erythrocyte malaria parasites generate nascent membranous structures which serve as a pathway for parasite protein transport to modify the host cell. The molecular basis of such membranous structures is not well understood, particularly for malaria parasites other than Plasmodium falciparum. To characterize the structural basis of protein trafficking in the Plasmodium knowlesi-infected erythrocyte, we identified a P. knowlesi ortholog of MAHRP2, a marker of the tether structure that connects membranous structures in the P...
April 16, 2018: Parasitology International
Jiamei Le, Weiping Jia, Yongning Sun
Mitochondrial dysfunction is mainly associated with high-fat-diet (HFD)-induced hepatic steatosis. Sennoside A (SA), a commonly used clinical stimulant laxative, is reported to improve energy metabolism and insulin resistance. However, the effect and mechanism of SA on HFD-induced hepatic steatosis remain largely unknown. The aim of this study was to determine the effect and mechanism of SA on HFD-induced hepatic steatosis in mice. We examined the liver and body weight of mice to evaluate the physical changes in the liver...
April 16, 2018: Biochemical and Biophysical Research Communications
J Kent Blasie
The mechanism of electromechanical coupling for voltage-gated ion channels (VGICs) involved in neurological signal transmission, primarily Nav- and Kv-channels, remains unresolved. Anesthetics have been shown to directly impact this mechanism, at least for Kv-channels. Molecular dynamics computer simulations can now predict the structures of VGICs embedded within a hydrated phospholipid bilayer membrane as a function of the applied transmembrane voltage, but significant assumptions are still necessary. Nevertheless, these simulations are providing new insights into the mechanism of electromechanical coupling at the atomic level in 3-D...
2018: Methods in Enzymology
Patrick J Loll
Anesthetics interact with a broad range of different targets, including both soluble and membrane-bound proteins. Understanding these interactions at the molecular level requires detailed structural knowledge of anesthetic-protein complexes, and one of the most productive routes to such knowledge is X-ray crystallography. In this chapter we discuss the application of this technique to the analysis of complexes of anesthetics with soluble proteins. The model protein apoferritin is highlighted, and protocols are presented for obtaining diffraction-quality crystals of this protein in complex with different general anesthetics...
2018: Methods in Enzymology
Michael L Barta, Shoichi Tachiyama, Meenakumari Muthuramalingam, Olivia Arizmendi, Cecilia E Villanueva, Kasra X Ramyar, Brian V Geisbrecht, Scott Lovell, Kevin P Battaile, Wendy L Picking, William D Picking
Bacterial type III secretion systems (T3SS) are used to inject proteins into mammalian cells to subvert cellular functions. The Shigella T3SS apparatus (T3SA) is comprised of a basal body, cytoplasmic sorting platform and exposed needle with needle "tip complex" (TC). TC maturation occurs when the translocator protein IpaB is recruited to the needle tip where both IpaD and IpaB control secretion induction. IpaB insertion into the host membrane is the first step of translocon pore formation and secretion induction...
April 19, 2018: Protein Science: a Publication of the Protein Society
Kathryn M Schultz, Matthew A Fischer, Elizabeth L Noey, Candice S Klug
Lipopolysaccharide (LPS) is an essential element of nearly all Gram-negative bacterial outer membranes and serves to protect the cell from adverse environmental stresses. Seven members of the lipopolysaccharide transport (Lpt) protein family function together to transport LPS from the inner membrane (IM) to the outer leaflet of the outer membrane of bacteria such as Escherichia coli. Each of these proteins has a solved crystal structure, including LptC, which is a largely periplasmic protein that is associated with the IM LptB2 FG complex and anchored to the membrane by an N-terminal helix...
April 19, 2018: Protein Science: a Publication of the Protein Society
Eamonn Reading
Mass spectrometry has emerged as an important structural biology tool for understanding membrane protein structure, function, and dynamics. Generally, structural mass spectrometry of membrane proteins has been performed on purified or reconstituted systems which lack the native lipid membrane and cellular environments. However, there has been progress in the use and adaptations of these methods for probing membrane proteins within increasingly more native contexts. In this Concept article the use and utility of structural mass spectrometry techniques for studying membrane proteins within native environments are highlighted...
April 19, 2018: Chemistry: a European Journal
Michaela Frolikova, Pavla Manaskova-Postlerova, Jiri Cerny, Jana Jankovicova, Ondrej Simonik, Alzbeta Pohlova, Petra Secova, Jana Antalikova, Katerina Dvorakova-Hortova
Proteins CD9 and CD81 are members of the tetraspanin superfamily and were detected in mammalian sperm, where they are suspected to form an active tetraspanin web and to participate in sperm⁻egg membrane fusion. The importance of these two proteins during the early stages of fertilization is supported by the complete sterility of CD9/CD81 double null female mice. In this study, the putative mechanism of CD9/CD81 involvement in tetraspanin web formation in sperm and its activity prior to fertilization was addressed...
April 19, 2018: International Journal of Molecular Sciences
Abhilasha Sood, Arpit Mehrotra, Devinder K Dhawan, Rajat Sandhir
Stroke is an increasingly prevalent clinical condition and second leading cause of death globally. The present study evaluated the therapeutic potential of Indian Ginseng, also known as Withania somnifera (WS), supplementation on middle cerebral artery occlusion (MCAO) induced mitochondrial dysfunctions in experimental model of ischemic stroke. Stroke was induced in animals by occluding the middle cerebral artery, followed by reperfusion injury. Ischemia reperfusion injury resulted in increased oxidative stress indicated by increased reactive oxygen species and protein carbonyl levels; compromised antioxidant system; in terms of reduced superoxide dismutase and catalase activity, along with reduction in GSH levels and the redox ratio, impaired mitochondrial functions and enhanced expression of apoptosis markers...
April 18, 2018: Metabolic Brain Disease
Medhat Wahba Shafaa, Amany Hasan Elshazly, Amira Zaki Dakrory, Maha Reda Elsyed
Purpose: To stress the influence of Coenzyme Q10 (CoQ10) on the structural properties of liposomes as model membranes and to investigate the possible role of CoQ10 or CoQ10 doped in liposomes when topically instilled as eye drops, in preventing cataract. Methods: The molecular interaction between liposomes and Coenzyme Q10 was examined using differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopy (FTIR). Rat pups were randomly divided into six groups comprising 15 pups. Group (1), control group...
March 2018: Advanced Pharmaceutical Bulletin
Masato Kaneda, Shinsaku Kawaguchi, Nobutaka Fujii, Hiroaki Ohno, Shinya Oishi
Odoamide is a cytotoxic peptide-polyketide hybrid molecule isolated from the Okinawan marine cyanobacterium Okeania sp. For an efficient structure-activity relationship study of the peptide part of odoamide, a facile synthetic protocol was established using a solid-phase peptide synthesis. Among a series of peptides, the d-MeAla6 isomer exhibited a more potent cytotoxicity than natural odoamide. It was also demonstrated that the 26-membered macrocyclic natural odoamide and the 24-membered isomer with comparable cytotoxicities were slowly interconvertible, and both isomers contributed to the potent cytotoxicity of odoamide...
April 12, 2018: ACS Medicinal Chemistry Letters
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