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Membrane protein crystal structure

Zhenning Ren, Jumin Lee, Mahdi Muhammad Moosa, Yin Nian, Liya Hu, Zhichun Xu, Jason G McCoy, Allan Chris M Ferreon, Wonpil Im, Ming Zhou
The phosphoenolpyruvate-dependent phosphotransferase system (PTS) transports sugar into bacteria and phosphorylates the sugar for metabolic consumption. The PTS is important for the survival of bacteria and thus a potential target for antibiotics, but its mechanism of sugar uptake and phosphorylation remains unclear. The PTS is composed of multiple proteins, and the membrane-embedded Enzyme IIC (EIIC) component transports sugars across the membrane. Crystal structures of two members of the glucose superfamily of EIICs, bcChbC and bcMalT, were solved in the inward-facing and outward-facing conformations, and the structures suggest that sugar translocation could be achieved by movement of a structured domain that contains the sugar-binding site...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
James Birch, Danny Axford, James Foadi, Arne Meyer, Annette Eckardt, Yvonne Thielmann, Isabel Moraes
Integral membrane proteins are among the most fascinating and important biomolecules as they play a vital role in many biological functions. Knowledge of their atomic structures is fundamental to the understanding of their biochemical function and key in many drug discovery programs. However, over the years, structure determination of integral membrane proteins has proven to be far from trivial, hence they are underrepresented in the protein data bank. Low expression levels, insolubility and instability are just a few of the many hurdles one faces when studying these proteins...
May 17, 2018: Methods: a Companion to Methods in Enzymology
Kangsa Amporndanai, Rachel M Johnson, Paul M O'Neill, Colin W G Fishwick, Alexander H Jamson, Shaun Rawson, Stephen P Muench, S Samar Hasnain, Svetlana V Antonyuk
Cytochrome bc 1 , a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochrome bc 1 from mammalian homologues co-crystallized with lead compounds have underpinned structure-based drug design to develop compounds with higher potency and selectivity. However, owing to the limited amount of cytochrome bc 1 that may be available from parasites, all efforts have been focused on homologous cytochrome bc 1 complexes from mammalian species, which has resulted in the failure of some drug candidates owing to toxicity in the host...
March 1, 2018: IUCrJ
Pavol Skubák, Demet Araç, Matthew W Bowler, Ana R Correia, Andre Hoelz, Sine Larsen, Gordon A Leonard, Andrew A McCarthy, Sean McSweeney, Christoph Mueller-Dieckmann, Harm Otten, Gabriel Salzman, Navraj S Pannu
Determining macromolecular structures from X-ray data with resolution worse than 3 Å remains a challenge. Even if a related starting model is available, its incompleteness or its bias together with a low observation-to-parameter ratio can render the process unsuccessful or very time-consuming. Yet, many biologically important macromolecules, especially large macromolecular assemblies, membrane proteins and receptors, tend to provide crystals that diffract to low resolution. A new algorithm to tackle this problem is presented that uses a multivariate function to simultaneously exploit information from both an initial partial model and low-resolution single-wavelength anomalous diffraction data...
March 1, 2018: IUCrJ
Stefan Taube, Alvaro Mallagaray, Thomas Peters
Noroviruses engage glycans as essential attachment factors to promote infection of host cells. The past decade has witnessed significant progress in the field of norovirus research. Cell culture systems and animal models have become available, and structural biology and biophysics have significantly expanded our understanding of norovirus-glycan interactions. From crystallography, many high-resolution crystal structures are now available disclosing key elements of glycan recognition at atomic resolution. On this basis, NMR spectroscopy, native mass spectrometry, and biophysical techniques targeting membrane attached glycans have raised more intricate questions about the nature of norovirus-glycan attachment implying that a static picture of glycan recognition is insufficient...
May 10, 2018: Current Opinion in Virology
Amira A Goda, Abu Bakar Siddique, Mohamed Mohyeldin, Nehad M Ayoub, Khalid A El Sayed
Breast cancer (BC) is a heterogeneous disease with different molecular subtypes. The high conductance calcium-activated potassium channels (BK, Maxi-K channels) play an important role in the survival of some BC phenotypes, via membrane hyperpolarization and regulation of cell cycle. BK channels have been implicated in BC cell proliferation and invasion. Penitrems are indole diterpene alkaloids produced by various terrestrial and marine Penicillium species. Penitrem A ( 1 ) is a selective BK channel antagonist with reported antiproliferative and anti-invasive activities against multiple malignancies, including BC...
May 11, 2018: Marine Drugs
Soo Y Ro, Matthew O Ross, Yue Wen Deng, Sharon Batelu, Thomas J Lawton, Joseph D Hurley, Timothy L Stemmler, Brian M Hoffman, Amy C Rosenzweig
Particulate methane monooxygenase (pMMO) is a copper-dependent, integral membrane metalloenzyme that converts methane to methanol in methanotrophic bacteria. Studies of isolated pMMO have been hindered by loss of enzymatic activity upon its removal from the native membrane. To characterize pMMO in a membrane-like environment, we reconstituted pMMOs from Methylococcus ( Mcc. ) capsulatus (Bath) and Methylomicrobium ( Mm. ) alcaliphilum 20Z into bicelles. Reconstitution into bicelles recovers methane oxidation activity lost upon detergent solubilization and purification without substantial alterations to copper content or copper electronic structure as observed by electron paramagnetic resonance (EPR) spectroscopy...
May 8, 2018: Journal of Biological Chemistry
Simone Furini, Carmen Domene
Since the availability of the first crystal structure of a bacterial Na+ channel in 2011, understanding selectivity across this family of membrane proteins has been the subject of intense research efforts. Initially, free energy calculations based on molecular dynamics simulations revealed that although sodium ions can easily permeate the channel with their first hydration shell almost intact, the selectivity filter is too narrow for efficient conduction of hydrated potassium ions. This steric view of selectivity was subsequently questioned by microsecond atomic trajectories, which proved that the selectivity filter appears to the permeating ions as a highly degenerate, liquid-like environment...
May 7, 2018: Proceedings of the National Academy of Sciences of the United States of America
Jungang Deng, Jun Wang, MuhammadHamid Khan, Ping Yu, Feng Yang, Hong Liang
We synthesized and validated five Schiff base Pt(II) complexes derived from 2-hydroxy-1-naphthaldehyde benzoyl hydrazone and its derivatives, which are modified at the benzohydrazide structures (L1-L5). The complexes were [Pt(L1)(DMSO)Cl] (C1), [Pt(L2)(DMSO)Cl] (C2), [Pt(L3)(DMSO)Cl] (C3), [Pt(L4)(DMSO)Cl] (C4), and [Pt(L5)(DMSO)Cl] (C5). Crystal structures showed that the Pt centers of all complexes were tetra-coordinated with other atoms. The structure-activity relationships and anticancer mechanisms of the complexes were explored...
April 25, 2018: Journal of Inorganic Biochemistry
Baohua Chen, Yun Zhu, Sheng Ye, Rongguang Zhang
Myelin-gene regulatory factor (MYRF) is a membrane-bound transcription factors, which is responsible for the differentiation of oligodendrocytes and myelination of central nervous system. Followed by a self-cleavage by the intramolecular chaperone auto-processing (ICA) domain, DNA-binding domain (DBD) of MYRF is released from the endoplasmic reticulum (ER) and translocated to the nucleus to regulate gene expression. In present work, we have solved the crystal structure of the human MYRF-DBD to 1.85-Å resolution...
May 2, 2018: Journal of Structural Biology
Raphael D Teixeira, Cristiane R Guzzo, Santiago Justo Arévalo, Maxuel O Andrade, Josielle Abrahão, Robson F de Souza, Chuck S Farah
The second messenger cyclic diguanylate monophosphate (c-di-GMP) is a central regulator of bacterial lifestyle, controlling several behaviors, including the switch between sessile and motile states. C-di-GMP levels are controlled by the interplay between diguanylate cyclases (DGCs) and phosphodiesterases (PDEs), which synthesize and hydrolyze this second messenger, respectively. These enzymes often contain additional domains that regulate activity via binding of small molecules, covalent modification or protein-protein interactions...
May 4, 2018: Journal of Biological Chemistry
Mareike G Posner, Abhishek Upadhyay, Rieko Ishima, Antreas C Kalli, Gemma Harris, Joachim Kremerskothen, Mark S P Sansom, Susan J Crennell, Stefan Bagby
KIBRA, a multi-functional scaffold protein with around twenty known binding partners, is involved in memory and cognition, organ size control via the Hippo pathway, cell polarity, and membrane trafficking. KIBRA includes tandem N-terminal WW domains, a C2 domain and motifs for binding aPKC and PDZ domains. A naturally occurring human KIBRA variant involving residue changes at positions 734 (M-to-I) and 735 (S-to-A) within the C2 domain affects cognitive performance. We have elucidated 3D structures, and calcium and phosphoinositide binding properties, of human KIBRA C2 domain...
May 3, 2018: Journal of Biological Chemistry
Alisa Ferofontov, Roi Strulovich, Milit Marom, Moshe Giladi, Yoni Haitin
Chloride intracellular channels (CLICs) are a family of unique proteins, that were suggested to adopt both soluble and membrane-associated forms. Moreover, following this unusual metamorphic change, CLICs were shown to incorporate into membranes and mediate ion conduction in vitro, suggesting multimerization upon membrane insertion. Here, we present a 1.8 Å resolution crystal structure of the CLIC domain of mouse CLIC6 (mCLIC6). The structure reveals a monomeric arrangement and shows a high degree of structural conservation with other CLICs...
May 2, 2018: Scientific Reports
Tomoya Tsukazaki
The bacterial membrane protein SecDF enhances protein translocation across the membrane driven by the complex of SecA ATPase and SecYEG. Many newly synthesized proteins in the cytoplasm are programmed to be translocated to the periplasm via the narrow channel that is formed in the center of SecYEG. During the protein translocation process, SecDF is proposed to undergo repeated conformational transitions to pull out the precursor protein from the SecYEG channel into the periplasm. Once SecDF captures the precursor protein on the periplasmic surface, SecDF can complete protein translocation even if SecA function is inactivated by ATP depletion, implying that SecDF is a protein translocation motor that works independent of SecA...
April 27, 2018: FEMS Microbiology Letters
Yong Ju Kim
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme, catalyses the conversion of D-glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate. While mammalian and yeast GAPDHs are multifunctional proteins that have additional functions beyond those involved in glycolysis, including reactions related to nuclear RNA transport, DNA replication/repair, membrane fusion and cellular apoptosis, Escherichia coli GAPDH (ecGAPDH) has only been reported to function in glycolysis. The S-loop of GAPDH is required for interaction with its cofactor and with other proteins...
May 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
Lautaro D Alvarez, Adali Pecci
Neurosteroids are the principal endogenous modulators of the γ-Aminobutyric acid receptors (GABAA Rs), pentameric membrane-bound proteins that can be assembled from at least 19 subunits. In the most abundant GABAA R arrangement (α1 β2 γ2 ), neurosteroids can potentiate the GABA action as well as produce a direct activation of the channel. The recent crystal structures of neurosteroids bound to α homopentameric GABAA R reveal binding to five equivalent sites. However, these results have been obtained using receptors that are not physiologically relevant, suggesting a need to investigate neurosteroid binding to heteropentameric receptors that exist in the central nervous system...
April 26, 2018: Journal of Steroid Biochemistry and Molecular Biology
Yen-Ting Lai, Hirotsugu Ogi, Kentaro Noi, Fumihito Kato
Unlike previous in-vitro measurements where Aβ aggregation was studied in bulk solutions, we detect the structure change of the Aβ aggregate on the surface of a wireless quartz-crystal-microbalance biosensor, which resembles more closely the aggregation process on the cell membrane. Using a 58-MHz quartz crystal, we monitored changes in the viscoelastic properties of the aggregate formed on the quartz surface from monomers to oligomers and then to fibrils, involving up to the 7th overtone mode (406 MHz). With atomic-force-microscopy observations, we found significant stiffness increase as well as thinning of the protein layer during the structure change from oligomer to fibrils at ~20 h, which indicates that the stiffness of the fibril is much higher...
April 26, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Melanie H Dietrich, Kristen M Ogden, Jacob M Long, Rebecca Ebenhoch, Alexandra Thor, Terence S Dermody, Thilo Stehle
Mammalian orthoreovirus attachment to target cells is mediated by outer-capsid protein σ1, which projects from the virion surface. The σ1 protein is a homotrimer consisting of a filamentous tail, which is partly inserted into the virion, a body domain constructed from β-spiral repeats, and a globular head with receptor-binding properties. The σ1 tail is predicted to form an α-helical coiled coil. Although σ1 undergoes a conformational change during cell entry, the nature of this change and its contributions to viral replication are unknown...
April 25, 2018: Journal of Virology
Nathanial R Eddy, José N Onuchic
Class I viral fusion proteins are α-helical proteins that facilitate membrane fusion between viral and host membranes through large conformational transitions. Although prefusion and postfusion crystal structures have been solved for many of these proteins, details about how they transition between these states have remained elusive. This work presents the first, to our knowledge, computational survey of transitions between pre- and postfusion configurations for several class I viral fusion proteins using structure-based models to analyze their dynamics...
April 24, 2018: Biophysical Journal
Ahmad Gebai, Alexei Gorelik, Zixian Li, Katalin Illes, Bhushan Nagar
Acid ceramidase (aCDase, ASAH1) hydrolyzes lysosomal membrane ceramide into sphingosine, the backbone of all sphingolipids, to regulate many cellular processes. Abnormal function of aCDase leads to Farber disease, spinal muscular atrophy with progressive myoclonic epilepsy, and is associated with Alzheimer's, diabetes, and cancer. Here, we present crystal structures of mammalian aCDases in both proenzyme and autocleaved forms. In the proenzyme, the catalytic center is buried and protected from solvent. Autocleavage triggers a conformational change exposing a hydrophobic channel leading to the active site...
April 24, 2018: Nature Communications
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