scholarly journals Structural Basis for the Distinct Membrane Binding Activity of the Homologous C2A Domains of Myoferlin and Dysferlin

2019 ◽  
Vol 431 (11) ◽  
pp. 2112-2126 ◽  
Author(s):  
Faraz M. Harsini ◽  
Anthony A. Bui ◽  
Anne M. Rice ◽  
Sukanya Chebrolu ◽  
Kerry L. Fuson ◽  
...  
Keyword(s):  
Membrane Binding ◽  
Binding Activity ◽  
Structural Basis ◽  
Distinct Membrane

scholarly journals Crystallization of and selenomethionine phasing strategy for a SETMAR–DNA complex

2016 ◽  
Vol 72 (9) ◽  
pp. 713-719 ◽  
Author(s):  
Qiujia Chen ◽  
Millie Georgiadis
Keyword(s):  
Dna Binding ◽  
Catalytic Domain ◽  
Specific Binding ◽  
Critical Role ◽  
Binding Activity ◽  
Structural Basis ◽  
Unexpected Finding ◽  
Terminal Inverted Repeat ◽  
Dna Binding Activity ◽  
New Genes

Transposable elements have played a critical role in the creation of new genes in all higher eukaryotes, including humans. Although the chimeric fusion protein SETMAR is no longer active as a transposase, it contains both the DNA-binding domain (DBD) and catalytic domain of theHsmar1transposase. The amino-acid sequence of the DBD has been virtually unchanged in 50 million years and, as a consequence, SETMAR retains its sequence-specific binding to the ancestralHsmar1terminal inverted repeat (TIR) sequence. Thus, the DNA-binding activity of SETMAR is likely to have an important biological function. To determine the structural basis for the recognition of TIR DNA by SETMAR, the design of TIR-containing oligonucleotides and SETMAR DBD variants, crystallization of DBD–DNA complexes, phasing strategies and initial phasing experiments are reported here. An unexpected finding was that oligonucleotides containing two BrdUs in place of thymidines produced better quality crystals in complex with SETMAR than their natural counterparts.

scholarly journals CTP regulates membrane-binding activity of the nucleoid occlusion protein Noc

2021 ◽  
Author(s):  
Adam S.B. Jalal ◽  
Ngat T. Tran ◽  
Ling J. Wu ◽  
Karunakaran Ramakrishnan ◽  
Martin Rejzek ◽  
...  
Keyword(s):  
Membrane Binding ◽  
Binding Activity

scholarly journals Structural, functional and computational studies of membrane recognition by Plasmodium Perforin-Like Proteins 1 and 2.

2021 ◽  
Author(s):  
Sophie Williams ◽  
Xiulian Yu ◽  
Tao Ni ◽  
Robert Gilbert ◽  
Phillip Stansfeld
Keyword(s):  
Life Cycle ◽  
Lipid Bilayers ◽  
Membrane Binding ◽  
Binding Activity ◽  
Life Cycles ◽  
Site Directed Mutagenesis ◽  
Parasite Life Cycle ◽  
Dynamics Simulations ◽  
Membrane Recognition

Perforin-like proteins (PLPs) play key roles in the mechanisms associated with parasitic disease caused by apicomplexans such as Plasmodium (malaria) and Toxoplasma. The T. gondii PLP1 (TgPLP1) mediates tachyzoite egress from cells, while the five Plasmodium PLPs carry out various roles in the life cycle of the parasite and with respect to the molecular basis of disease. Here we focus on Plasmodium vivax PLP1 and PLP2 (PvPLP1 and PvPLP2) compared to TgPLP1; PvPLP1 is important for invasion of mammalian hosts by the parasite and establishment of a chronic infection, PvPLP2 is important during the symptomatic blood stage of the parasite life cycle. Determination of the crystal structure of the membrane-binding APCβ domain of PvPLP1 reveals notable differences with that of TgPLP1, which are reflected in its inability to bind lipid bilayers in the way that TgPLP1 and PvPLP2 can be shown to. Molecular dynamics simulations combined with site-directed mutagenesis and functional assays allow a dissection of the binding interactions of TgPLP1 and PvPLP2 on lipid bilayers, and reveal a similar tropism for lipids found enriched in the inner leaflet of the mammalian plasma membrane. In addition to this shared mode of membrane binding PvPLP2 displays a secondary synergistic interaction side-on from its principal bilayer interface. This study underlines the substantial differences between the biophysical properties of the APCβ domains of Apicomplexan PLPs, which reflect their significant sequence diversity. Such differences will be important factors in determining the cell targeting and membrane-binding activity of the different proteins, in their different developmental roles within parasite life cycles.

scholarly journals Coordinated autoinhibition of F-BAR domain membrane binding and WASp activation by Nervous Wreck

2016 ◽  
Vol 113 (38) ◽  
pp. E5552-E5561 ◽  
Author(s):  
Tatiana B. Stanishneva-Konovalova ◽  
Charlotte F. Kelley ◽  
Tania L. Eskin ◽  
Emily M. Messelaar ◽  
Steven A. Wasserman ◽  
...  
Keyword(s):  
Bound States ◽  
Membrane Binding ◽  
Structural Basis ◽  
Synaptic Growth ◽  
Sh3 Domains ◽  
Actin Organization ◽  
Bar Domain ◽  
Src Homology

Membrane remodeling by Fes/Cip4 homology-Bin/Amphiphysin/Rvs167 (F-BAR) proteins is regulated by autoinhibitory interactions between their SRC homology 3 (SH3) and F-BAR domains. The structural basis of autoregulation, and whether it affects interactions of SH3 domains with other cellular ligands, remain unclear. Here we used single-particle electron microscopy to determine the structure of the F-BAR protein Nervous Wreck (Nwk) in both soluble and membrane-bound states. On membrane binding, Nwk SH3 domains do not completely dissociate from the F-BAR dimer, but instead shift from its concave surface to positions on either side of the dimer. Unexpectedly, along with controlling membrane binding, these autoregulatory interactions inhibit the ability of Nwk-SH3a to activate Wiskott–Aldrich syndrome protein (WASp)/actin related protein (Arp) 2/3-dependent actin filament assembly. In Drosophila neurons, Nwk autoregulation restricts SH3a domain-dependent synaptopod formation, synaptic growth, and actin organization. Our results define structural rearrangements in Nwk that control F-BAR–membrane interactions as well as SH3 domain activities, and suggest that these two functions are tightly coordinated in vitro and in vivo.

scholarly journals Structural and functional analysis of the human spliceosomal DEAD-box helicase Prp28

2014 ◽  
Vol 70 (6) ◽  
pp. 1622-1630 ◽  
Author(s):  
Sina Möhlmann ◽  
Rebecca Mathew ◽  
Piotr Neumann ◽  
Andreas Schmitt ◽  
Reinhard Lührmann ◽  
...  
Keyword(s):  
Binding Activity ◽  
Mrna Splicing ◽  
Structural Basis ◽  
Atp Binding ◽  
Helicase Domain ◽  
Crucial Step ◽  
Closed Conformation ◽  
Dead Box ◽  
Open Conformation ◽  
U1 Snrnp

The DEAD-box protein Prp28 is essential for pre-mRNA splicing as it plays a key role in the formation of an active spliceosome. Prp28 participates in the release of the U1 snRNP from the 5′-splice site during association of the U5·U4/U6 tri-snRNP, which is a crucial step in the transition from a pre-catalytic spliceosome to an activated spliceosome. Here, it is demonstrated that the purified helicase domain of human Prp28 (hPrp28ΔN) binds ADP, whereas binding of ATP and ATPase activity could not be detected. ATP binding could not be observed for purified full-length hPrp28 either, but within an assembled spliceosomal complex hPrp28 gains ATP-binding activity. In order to understand the structural basis for the ATP-binding deficiency of isolated hPrp28, the crystal structure of hPrp28ΔN was determined at 2.0 Å resolution. In the crystal the helicase domain adopts a wide-open conformation, as the two RecA-like domains are extraordinarily displaced from the productive ATPase conformation. Binding of ATP is hindered by a closed conformation of the P-loop, which occupies the space required for the γ-phosphate of ATP.

The structural basis for membrane binding and pore formation by lymphocyte perforin

Nature ◽  
2010 ◽  
Vol 468 (7322) ◽  
pp. 447-451 ◽  
Author(s):  
Ruby H. P. Law ◽  
Natalya Lukoyanova ◽  
Ilia Voskoboinik ◽  
Tom T. Caradoc-Davies ◽  
Katherine Baran ◽  
...  
Keyword(s):  
Pore Formation ◽  
Membrane Binding ◽  
Structural Basis

Structural basis for the DNA-binding activity of the bacterial β-propeller protein YncE

2011 ◽  
Vol 67 (12) ◽  
pp. 1045-1053 ◽  
Author(s):  
Wataru Kagawa ◽  
Tomohiko Sagawa ◽  
Hironori Niki ◽  
Hitoshi Kurumizaka
Keyword(s):  
Dna Binding ◽  
Binding Activity ◽  
Structural Basis ◽  
Dna Binding Activity

scholarly journals F-actin binds to the cytoplasmic surface of ponticulin, a 17-kD integral glycoprotein from Dictyostelium discoideum plasma membranes.

1987 ◽  
Vol 105 (4) ◽  
pp. 1741-1751 ◽  
Author(s):  
L J Wuestehube ◽  
E J Luna
Keyword(s):  
Plasma Membrane ◽  
Binding Site ◽  
Dictyostelium Discoideum ◽  
Plasma Membranes ◽  
Membrane Binding ◽  
Binding Activity ◽  
Actin Binding ◽  
Actin Binding Protein ◽  
Cytoplasmic Surface ◽  
Actin Binding Site

F-actin affinity chromatography and immunological techniques are used to identify actin-binding proteins in purified Dictyostelium discoideum plasma membranes. A 17-kD integral glycoprotein (gp17) consistently elutes from F-actin columns as the major actin-binding protein under a variety of experimental conditions. The actin-binding activity of gp17 is identical to that of intact plasma membranes: it resists extraction with 0.1 N NaOH, 1 mM dithiothreitol (DTT); it is sensitive to ionic conditions; it is stable over a wide range of pH; and it is eliminated by proteolysis, denaturation with heat, or treatment with DTT and N-ethylmaleimide. gp17 may be responsible for much of the actin-binding activity of plasma membranes since monovalent antibody fragments (Fab) directed primarily against gp17 inhibit actin-membrane binding by 96% in sedimentation assays. In contrast, Fab directed against cell surface determinants inhibit binding by only 0-10%. The actin-binding site of gp17 appears to be located on the cytoplasmic surface of the membrane since Fab against this protein continue to inhibit 96% of actin-membrane binding even after extensive adsorption against cell surfaces. gp17 is abundant in the plasma membrane, constituting 0.4-1.0% of the total membrane protein. A transmembrane orientation of gp17 is suggested since, in addition to the cytoplasmic localization of the actin-binding site, extracellular determinants of gp17 are identified. gp17 is surface-labeled by sulfo-N-hydroxy-succinimido-biotin, a reagent that cannot penetrate the cell membrane. Also, gp17 is glycosylated since it is specifically bound by the lectin, concanavalin A. We propose that gp17 is a major actin-binding protein that is important for connecting the plasma membrane to the underlying microfilament network. Therefore, we have named this protein "ponticulin" from the Latin word, ponticulus, which means small bridge.

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