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  • 1. Andersson, Magnus
    et al.
    Vincent, Jonathan
    Uppsala Univ, Dept Photochem & Mol Sci.
    van der Spoel, David
    Davidsson, Jan
    Neutze, Richard
    A Proposed Time-Resolved X-Ray Scattering Approach to Track Localand Global Conformational Changes in Membrane Transport Proteins2008In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 16, p. 21-28Article in journal (Refereed)
    Abstract [en]

    Time-resolved X-ray scattering has emerged as a powerful technique for studying the rapid structural dynamics of small molecules in solution. Membrane-protein-catalyzed transport processes frequently couple large-scale conformational changes of the transporter with local structural changes perturbing the uptake and release of the transported substrate. Using light-driven halide ion transport catalyzed by halorhodopsin as a model system, we combine molecular dynamics simulations with X-ray scattering calculations to demonstrate how small-molecule time-resolved X-ray scattering can be extended to the study of membrane transport processes. In particular, by introducing strongly scattering atoms to label specific positions within the protein and substrate, the technique of time-resolved wide-angle X-ray scattering can reveal both local and global conformational changes. This approach simultaneously enables the direct visualization of global rearrangements and substrate movement, crucial concepts that underpin the alternating access paradigm for membrane transport proteins.

  • 2.
    Cisneros, David A.
    et al.
    Biotechnology Center, University of Technology, Dresden, Germany.
    Oberbarnscheidt, Leoni
    Pannier, Angela
    Klare, Johann P.
    Helenius, Jonne
    Engelhard, Martin
    Oesterhelt, Filipp
    Muller, Daniel J.
    Transducer binding establishes localized interactions to tune sensory rhodopsin II2008In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 16, no 8, p. 1206-1213Article in journal (Refereed)
    Abstract [en]

    In haloarchaea, sensory rhodopsin II (SRII) mediates a photophobic response to avoid photo-oxidative damage in bright light. Upon light activation the receptor undergoes a conformational change that activates a tightly bound transducer molecule (HtrII), which in turn by a chain of homologous reactions transmits the signal to the chemotactic eubacterial two-component system. Here, using single-molecule force spectroscopy, we localize and quantify changes to the intramolecular interactions within SRII of Natronomonas pharaonis (NpSRII) upon NpHtrII binding. Transducer binding affected the interactions at transmembrane alpha helices F and G of NpSRII to which the transducer was in contact. Remarkably, the interactions were distributed asymmetrically and significantly stabilized alpha helix G entirely but alpha helix F only at its extracellular tip. These findings provide unique insights into molecular mechanisms that "prime" the complex for signaling, and guide the receptor toward transmitting light-activated structural changes to its cognate transducer.

  • 3.
    Cisneros, David A.
    et al.
    BIOTEC, University of Technology, 01307 Dresden, Germany..
    Oesterhelt, Dieter
    Müller, Daniel J
    Probing origins of molecular interactions stabilizing the membrane proteins halorhodopsin and bacteriorhodopsin2005In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 13, no 2, p. 235-242Article in journal (Refereed)
    Abstract [en]

    Single-molecule atomic force microscopy and spectroscopy were applied to detect molecular interactions stabilizing the structure of halorhodopsin (HR), a light-driven chloride pump from Halobacterium salinarum. Because of the high structural and sequence similarities between HR and bacteriorhodopsin, we compared their unfolding pathways and polypeptide regions that established structurally stable segments against unfolding. Unfolding pathways and structural segments stabilizing the proteins both exhibited a remarkably high similarity. This suggests that different amino acid compositions can establish structurally indistinguishable energetic barriers. These stabilizing domains rather result from comprehensive interactions of all amino acids within a structural region than from specific interactions. However, one additional unfolding barrier located within a short segment of helix E was detected for HR. This barrier correlated with a Pi-bulk interaction, which locally disrupts helix E and divides a structural stabilizing segment.

  • 4.
    Doran, Matthew H.
    et al.
    Department of Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, Boston, USA.
    Baker, Joseph L.
    Department of Chemistry, The College of New Jersey, Ewing, USA.
    Dahlberg, Tobias
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Bullitt, Esther
    Department of Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, Boston, USA.
    Three structural solutions for bacterial adhesion pilus stability and superelasticity2023In: Structure, ISSN 0969-2126, E-ISSN 1878-4186Article in journal (Refereed)
    Abstract [en]

    Bacterial adhesion pili are key virulence factors that mediate host-pathogen interactions in diverse epithelial environments. Deploying a multimodal approach, we probed the structural basis underpinning the biophysical properties of pili originating from enterotoxigenic (ETEC) and uropathogenic bacteria. Using cryo-electron microscopy we solved the structures of three vaccine target pili from ETEC bacteria, CFA/I, CS17, and CS20. Pairing these and previous pilus structures with force spectroscopy and steered molecular dynamics simulations, we find a strong correlation between subunit-subunit interaction energies and the force required for pilus unwinding, irrespective of genetic similarity. Pili integrate three structural solutions for stabilizing their assemblies: layer-to-layer interactions, N-terminal interactions to distant subunits, and extended loop interactions from adjacent subunits. Tuning of these structural solutions alters the biophysical properties of pili and promotes the superelastic behavior that is essential for sustained bacterial attachment.

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  • 5. Elmlund, Hans
    et al.
    Baraznenok, Vera
    Linder, Tomas
    Szilagyi, Zsolt
    Rofougaran, Reza
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Hofer, Anders
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Hebert, Hans
    Lindahl, Martin
    Gustafsson, Claes M
    Cryo-EM reveals promoter DNA binding and conformational flexibility of the general transcription factor TFIID2009In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 17, no 11, p. 1442-1452Article in journal (Refereed)
    Abstract [en]

    The general transcription factor IID (TFIID) is required for initiation of RNA polymerase II-dependent transcription at many eukaryotic promoters. TFIID comprises the TATA-binding protein (TBP) and several conserved TBP-associated factors (TAFs). Recognition of the core promoter by TFIID assists assembly of the preinitiation complex. Using cryo-electron microscopy in combination with methods for ab initio single-particle reconstruction and heterogeneity analysis, we have produced density maps of two conformational states of Schizosaccharomyces pombe TFIID, containing and lacking TBP. We report that TBP-binding is coupled to a massive histone-fold domain rearrangement. Moreover, docking of the TBP-TAF1(N-terminus) atomic structure to the TFIID map and reconstruction of a TAF-promoter DNA complex helps to account for TAF-dependent regulation of promoter-TBP and promoter-TAF interactions.

  • 6. Johansson, Renzo
    et al.
    Jonna, Venkateswara Rao
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Kumar, Rohit
    Nayeri, Niloofar
    Lundin, Daniel
    Sjöberg, Britt-Marie
    Hofer, Anders
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Logan, Derek T
    Structural Mechanism of Allosteric Activity Regulation in a Ribonucleotide Reductase with Double ATP Cones2016In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 24, no 6, p. 906-917Article in journal (Refereed)
    Abstract [en]

    Ribonucleotide reductases (RNRs) reduce ribonucleotides to deoxyribonucleotides. Their overall activity is stimulated by ATP and downregulated by dATP via a genetically mobile ATP cone domain mediating the formation of oligomeric complexes with varying quaternary structures. The crystal structure and solution X-ray scattering data of a novel dATP-induced homotetramer of the Pseudomonas aeruginosa class I RNR reveal the structural bases for its unique properties, namely one ATP cone that binds two dATP molecules and a second one that is non-functional, binding no nucleotides. Mutations in the observed tetramer interface ablate oligomerization and dATP-induced inhibition but not the ability to bind dATP. Sequence analysis shows that the novel type of ATP cone may be widespread in RNRs. The present study supports a scenario in which diverse mechanisms for allosteric activity regulation are gained and lost through acquisition and evolutionary erosion of different types of ATP cone.

  • 7.
    Jäger, Franziska
    et al.
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Lamy, Anaïs
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics. Umeå University, Faculty of Medicine, Wallenberg Centre for Molecular Medicine at Umeå University (WCMM).
    Sun, Wei-Sheng
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics. Umeå University, Faculty of Medicine, Wallenberg Centre for Molecular Medicine at Umeå University (WCMM).
    Guerini, Nina
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Berntsson, Ronnie
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics. Umeå University, Faculty of Medicine, Wallenberg Centre for Molecular Medicine at Umeå University (WCMM).
    Structure of the enterococcal T4SS protein PrgL reveals unique dimerization interface in the VirB8 protein family2022In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 30, no 6, p. 876-885.e5Article in journal (Refereed)
    Abstract [en]

    Multidrug-resistant bacteria pose serious problems in hospital-acquired infections (HAIs). Most antibiotic resistance genes are acquired via conjugative gene transfer, mediated by type 4 secretion systems (T4SS). Although most multidrug-resistant bacteria responsible for HAIs are of Gram-positive origin, with enterococci being major contributors, mostly Gram-negative T4SSs have been characterized. Here, we describe the structure and organization of PrgL, a core protein of the T4SS channel, encoded by the pCF10 plasmid from Enterococcus faecalis. The structure of PrgL displays similarity to VirB8 proteins of Gram-negative T4SSs. In vitro experiments show that the soluble domain alone is enough to drive both dimerization and dodecamerization, with a dimerization interface that differs from all other known VirB8-like proteins. In vivo experiments verify the importance of PrgL dimerization. Our findings provide insight into the molecular building blocks of Gram-positive T4SS, highlighting similarities but also unique features in PrgL compared to other VirB8-like proteins.

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  • 8. Manav, Melek Cemre
    et al.
    Turnbull, Kathryn Jane
    Department of Biology, University of Copenhagen, Centre for Bacterial Stress Response and Persistence, Copenhagen 2200, Denmark; Present address: Department of Molecular Biology, Umeå University, 901 87 Umeå , Sweden.
    Jurenas, Dukas
    Garcia-Pino, Abel
    Gerdes, Kenn
    Brodersen, Ditlev Egeskov
    The E. coli HicB Antitoxin Contains a Structurally Stable Helix-Turn-Helix DNA Binding Domain2019In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 27, no 11, p. 1675-+Article in journal (Refereed)
    Abstract [en]

    The E. coli hicAB type II toxin-antitoxin locus is unusual by being controlled by two promoters and by having the toxin encoded upstream of the antitoxin. HicA toxins contain a double-stranded RNA-binding fold and cleaves both mRNA and tmRNA in vivo, while HicB antitoxins contain a partial RNase H fold and either a helix-turn-helix (HTH) or ribbon-helix-helix domain. It is not known how an HTH DNA-binding domain affects higher-order structure for the HicAB modules. Here, we present crystal structures of the isolated E. coli HicB antitoxin and full-length HicAB complex showing that HicB forms a stable DNA-binding module and interacts in a canonical way with HicA despite the presence of an HTH-type DNA-binding domain. No major structural rearrangements take place upon binding of the toxin. Both structures expose well-ordered DNA-binding motifs allowing a model for DNA binding by the antitoxin to be generated.

  • 9. Park, Ah Young
    et al.
    Jergic, Slobodan
    Politis, Argyris
    Ruotolo, Brandon T
    Hirshberg, Daniel
    Jessop, Linda L
    Beck, Jennifer L
    Barsky, Daniel
    O'Donnell, Mike
    Dixon, Nicholas E
    Robinson, Carol V
    A single subunit directs the assembly of the Escherichia coli DNA sliding clamp loader.2010In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 18, no 3Article in journal (Refereed)
    Abstract [en]

    Multi-protein clamp loader complexes are required to load sliding clamps onto DNA. In Escherichia coli the clamp loader contains three DnaX (tau/gamma) proteins, delta, and delta', which together form an asymmetric pentameric ring that also interacts with psichi. Here we used mass spectrometry to examine the assembly and dynamics of the clamp loader complex. We find that gamma exists exclusively as a stable homotetramer, while tau is in a monomer-dimer-trimer-tetramer equilibrium. delta' plays a direct role in the assembly as a tau/gamma oligomer breaker, thereby facilitating incorporation of lower oligomers. With delta', both delta and psichi stabilize the trimeric form of DnaX, thus completing the assembly. When tau and gamma are present simultaneously, mimicking the situation in vivo, subunit exchange between tau and gamma tetramers occurs rapidly to form heterocomplexes but is retarded when deltadelta' is present. The implications for intracellular assembly of the DNA polymerase III holoenzyme are discussed.

  • 10. Shah, Claudio
    et al.
    Hegde, Balachandra G
    Morén, Björn
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Behrmann, Elmar
    Mielke, Thorsten
    Moenke, Gregor
    Spahn, Christian MT
    Lundmark, Richard
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Daumke, Oliver
    Langen, Ralf
    Structural insights into membrane interaction and caveolar targeting of dynamin-like EHD22014In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 22, no 3, p. 409-420Article in journal (Refereed)
    Abstract [en]

    The dynamin-related Eps15-homology domain-containing protein 2 (EHD2) is a membrane-remodeling ATPase that regulates the dynamics of caveolae. Here, we established an electron paramagnetic resonance (EPR) approach to characterize structural features of membrane-bound EHD2. We show that residues at the tip of the helical domain can insert into the membrane and may create membrane curvature by a wedging mechanism. Using EPR and X-ray crystallography, we found that the N terminus is folded into a hydrophobic pocket of the GTPase domain in solution and can be released into the membrane. Cryoelectron microscopy demonstrated that the N terminus is not essential for oligomerization of EHD2 into a membrane-anchored scaffold. Instead, we found a function of the N terminus in regulating targeting and stable association of EHD2 to caveolae. Our data uncover an unexpected, membrane-induced regulatory switch in EHD2 and demonstrate the versatility of EPR to study structure and function of dynamin superfamily proteins.

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