Institute of Biological Information Processing (IBI)

Structural Biochemistry (IBI-7)

Publications 2015

AlTarabeen, M. ; Daletos, G. ; Ebrahim, W. ; Müller, W. E. G. ; Hartmann, R. ; Lin, W. ; Proksch, P. (Corresponding author)
Ircinal E, a New Manzamine Derivative frim the Indonesian Marine Sponge Acanthostrongylophora ingens
Natural product communications 10, 1951-1953 (2015) special issue: "11"2015 Files BibTeX | EndNote: XML, Text | RIS

Bogorodskiy, A. ; Frolov, F. ; Mishin, A. ; Round, E. ; Polovinkin, V. ; Cherezov, V. ; Gordeliy, V. ; Büldt, G. ; Gensch, T. ; Borshchevskiy, V. (Corresponding author)
Nucleation and Growth of Membrane Protein Crystals In Meso —A Fluorescence Microscopy Study
Crystal growth & design 15(12), 5656 - 5660 (2015) [10.1021/acs.cgd.5b01061]2015 Files BibTeX | EndNote: XML, Text | RIS

Börger, C. ; Schünke, S. ; Lecher, J. ; Stoldt, M. ; Winkhaus, F. ; Kaupp, U. B. ; Willbold, D. (Corresponding author)
Resonance assignment of the ligand-free cyclic nucleotide-binding domain from the murine ion channel HCN$_{2}$
Biomolecular NMR assignments 9(2), 243 - 246 (2015) [10.1007/s12104-014-9583-x]2015 Files BibTeX | EndNote: XML, Text | RIS

Borshchevskiy, V. ; Round, E. ; Bertsova, Y. ; Polovinkin, V. ; Gushchin, I. ; Ishchenko, A. ; Kovalev, K. ; Mishin, A. ; Kachalova, G. ; Popov, A. ; Bogachev, A. ; Gordeliy, V. (Corresponding author)
Structural and functional investigation of flavin binding center of the NqrC subunit of sodium-translocating NADH:Quinone oxidoreductase from Vibrio harveyi
PLoS one 10(3), e0118548 (2015) [10.1371/journal.pone.0118548]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Bratanov, D. ; Balandin, T. ; Round, E. ; Shevchenko, V. ; Gushchin, I. ; Polovinkin, V. ; Borshchevskiy, V. ; Gordeliy, V. (Corresponding author)
An Approach to Heterologous Expression of Membrane Proteins. The Case of Bacteriorhodopsin
PLoS one 10(6), e0128390 - (2015) [10.1371/journal.pone.0128390]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Braun, T. ; Orlova, A. ; Valegård, K. ; Lindås, A.-C. ; Schröder, G. ; Egelman, E. H. (Corresponding author)
Archaeal actin from a hyperthermophile forms a single-stranded filament
Proceedings of the National Academy of Sciences of the United States of America 112(30), 9340 - 9345 (2015) [10.1073/pnas.1509069112]2015 Files BibTeX | EndNote: XML, Text | RIS

Brener, O. ; Dunkelmann, T. ; Gremer, L. ; van Groen, T. ; Mirecka, E. A. ; Kadish, I. ; Willuweit, A. ; Kutzsche, J. ; Jürgens, D. ; Rudolph, S. ; Tusche, M. ; Bongen, P. ; Pietruszka, J. ; Oesterhelt, F. ; Langen, K.-J. ; Demuth, H.-U. ; Janssen, A. ; Hoyer, W. ; Funke, S. A. ; Nagel-Steger, L. ; Willbold, D. (Corresponding author)
QIAD assay for quantitating a compound’s efficacy in elimination of toxic Aβ oligomers
Scientific reports 5, 13222 (2015) [10.1038/srep13222]2015 Files Fulltext Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Bulavin, L. A. ; Soloviov, D. V. ; Gordeliy, V. ; Svechnikova, O. S. ; Krasnikova, A. O. ; Kasian, N. A. ; Vashchenko, O. V. ; Lisetski, L. N. (Corresponding author)
Lyotropic model membrane structures of hydrated DPPC: DSC and small-angle X-ray scattering studies of phase transitions in the presence of membranotropic agents
Phase transitions 88(6), 582 - 592 (2015) [10.1080/01411594.2014.1002784]2015 BibTeX | EndNote: XML, Text | RIS

Carballo-Pacheco, M. ; Ismail, A. E. ; Strodel, B. (Corresponding author)
Oligomer Formation of Toxic and Functional Amyloid Peptides Studied with Atomistic Simulations
The journal of physical chemistry <Washington, DC> / B 119(30), 9696 - 9705 (2015) [10.1021/acs.jpcb.5b04822]2015 Files Fulltext BibTeX | EndNote: XML, Text | RIS

Daletos, G. ; Kalscheuer, R. ; Koliwer-Brandl, H. ; Hartmann, R. ; de Voogd, N. J. ; Wray, V. ; Lin, W. ; Proksch, P. (Corresponding author)
Callyaerins from the Marine Sponge Callyspongia aerizusa : Cyclic Peptides with Antitubercular Activity
Journal of natural products 78(8), 1910 - 1925 (2015) [10.1021/acs.jnatprod.5b00266]2015 Files Fulltext BibTeX | EndNote: XML, Text | RIS

Dammers, C. ; Gremer, L. ; Neudecker, P. ; Demuth, H.-U. ; Schwarten, M. ; Willbold, D. (Corresponding author)
Purification and Characterization of Recombinant N-Terminally Pyroglutamate-Modified Amyloid-β Variants and Structural Analysis by Solution NMR Spectroscopy
PLoS one 10(10), e0139710 (2015) [10.1371/journal.pone.0139710]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Dammers, C. ; Gremer, L. ; Reiß, K. ; Klein, A. N. ; Neudecker, P. ; Hartmann, R. ; Sun, N. ; Demuth, H.-U. ; Schwarten, M. ; Willbold, D. (Corresponding author)
Structural Analysis and Aggregation Propensity of Pyroglutamate Aβ(3-40) in Aqueous Trifluoroethanol
PLoS one 10(11), e0143647 (2015) [10.1371/journal.pone.0143647]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Endres, S. (Corresponding Author) ; Granzin, J. ; Circolone, F. ; Stadler, A. ; Krauss, U. ; Drepper, T. ; Svensson, V. ; Knieps-Grünhagen, E. ; Wirtz, A. ; Cousin, A. ; Tielen, P. ; Willbold, D. ; Jaeger, K.-E. ; Batra-Safferling, R.
Structure and function of a short LOV protein from the marine phototrophic bacterium Dinoroseobacter shibae
BMC microbiology 15(1), 30 (2015) [10.1186/s12866-015-0365-0]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Feldman, T. B. (Corresponding author) ; Ivankov, O. I. ; Murugova, T. N. ; Kuklin, A. I. ; Shelyakin, P. V. ; Yakovleva, M. A. ; Gordeliy, V. ; Belushkin, A. V. ; Ostrovsky, M. A.
Study of visual pigment rhodopsin supramolecular organization in photoreceptor membrane by small-angle neutron scattering method with contrast variation
Doklady biochemistry and biophysics 465(1), 420–423 (2015) [10.1134/S1607672915060186]2015 Files BibTeX | EndNote: XML, Text | RIS

Galkin, V. ; Orlova, A. ; Vos, M. ; Schröder, G. ; Egelman, E. (Corresponding Author)
Near-Atomic Resolution for One State of F-Actin
Structure 23(1), 173 - 182 (2015) [10.1016/j.str.2014.11.006]2015 Files Fulltext BibTeX | EndNote: XML, Text | RIS

Goossens, K. ; Prior, M. ; Pacheco, V. ; Willbold, D. ; Müllen, K. ; Enderlein, J. ; Hofkens, J. ; Gregor, I. (Corresponding author)
Accurate Diffusion Coefficients of Organosoluble Reference Dyes in Organic Media Measured by Dual-Focus Fluorescence Correlation Spectroscopy
ACS nano 9(7), 7360 - 7373 (2015) [10.1021/acsnano.5b02371]2015 Files BibTeX | EndNote: XML, Text | RIS

Granzin, J. ; Stadler, A. ; Cousin, A. ; Schlesinger, R. ; Batra-Safferling, R. (Corresponding author)
Structural evidence for the role of polar core residue Arg175 in arrestin activation
Scientific reports 5, 15808 (2015) [10.1038/srep15808]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Gushchin, I. ; Shevchenko, V. ; Polovinkin, V. ; Kovalev, K. ; Alekseev, A. ; Round, E. ; Borshchevskiy, V. ; Balandin, T. ; Popov, A. ; Gensch, T. ; Fahlke, C. ; Bamann, C. ; Willbold, D. ; Büldt, G. ; Bamberg, E. ; Gordeliy, V. (Corresponding Author)
Crystal structure of a light-driven sodium pump
Nature structural & molecular biology 22(5), 390-395 (2015) [10.1038/nsmb.3002]2015 Files BibTeX | EndNote: XML, Text | RIS

Hendler, R. W. ; Meuse, C. W. ; Gallagher, T. ; Labahn, J. ; Kubicek, J. ; Smith, P. D. ; Kakareka, J. W. (Corresponding author)
Stray Light Correction in the Optical Spectroscopy of Crystals
Applied spectroscopy 69(9), 1106 - 1111 (2015) [10.1366/14-07716]2015 Files BibTeX | EndNote: XML, Text | RIS

Hung, Y.-F. ; Schwarten, M. ; Schünke, S. ; Thiagarajan-Rosenkranz, P. ; Hoffmann, S. ; Sklan, E. H. ; Willbold, D. ; König, B. (Corresponding author)
Dengue virus NS4A cytoplasmic domain binding to liposomes is sensitive to membrane curvature
Biochimica et biophysica acta / Biomembranes 1848(5), 1119 - 1126 (2015) [10.1016/j.bbamem.2015.01.015]2015 Files BibTeX | EndNote: XML, Text | RIS

Hung, Y.-F. ; Schwarten, M. ; Hoffmann, S. ; Willbold, D. ; Sklan, E. ; König, B. (Corresponding author)
Amino Terminal Region of Dengue Virus NS4A Cytosolic Domain Binds to Highly Curved Liposomes
Viruses 7(7), 4119 - 4130 (2015) [10.3390/v7072812]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Jiang, N. ; Leithold, L. H. E. ; Post, J. ; Ziehm, T. ; Mauler, J. ; Gremer, L. ; Cremer, M. ; Schartmann, E. ; Shah, N. J. ; Kutzsche, J. ; Langen, K.-J. ; Breitkreutz, J. ; Willbold, D. (Corresponding author) ; Willuweit, A. (Corresponding author)
Preclinical Pharmacokinetic Studies of the Tritium Labelled D-Enantiomeric Peptide D3 Developed for the Treatment of Alzheimer´s Disease
PLoS one 10(6), e0128553 - (2015) [10.1371/journal.pone.0128553]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Kahlert, U. D. ; Koch, K. ; Suwala, A. K. ; Hartmann, R. ; Cheng, M. ; Maciaczyk, D. ; Willbold, D. ; Eberhart, C. G. ; Glunde, K. ; Maciaczyk, J. (Corresponding author)
The effect of neurosphere culture conditions on the cellular metabolism of glioma cells
Folia neuropathologica 3, 219 - 225 (2015) [10.5114/fn.2015.54422]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Kovacic, F. ; Mandrysch, A. ; Poojari, C. ; Strodel, B. ; Jaeger, K.-E. (Corresponding author)
Structural features determining thermal adaptation of esterases
Protein engineering design and selection 29(2), 65-76 (2015) [10.1093/protein/gzv061]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Liao, Q. ; Kamerlin, S. C. L. ; Strodel, B. (Corresponding author)
Development and Application of a Nonbonded Cu $^{2+}$ Model That Includes the Jahn–Teller Effect
The journal of physical chemistry letters 6(13), 2657 - 2662 (2015) [10.1021/acs.jpclett.5b01122]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Ma, P. ; Xue, Y. ; Coquelle, N. ; Haller, J. D. ; Yuwen, T. ; Ayala, I. ; Mikhailovskii, O. ; Willbold, D. ; Colletier, J.-P. (Corresponding author) ; Skrynnikov, N. R. (Corresponding author) ; Schanda, P. (Corresponding author)
Observing the overall rocking motion of a protein in a crystal
Nature Communications 6, 8361 (2015) [10.1038/ncomms9361]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Ma, P. ; Schillinger, O. ; Schwarten, M. ; Lecher, J. ; Hartmann, R. ; Stoldt, M. ; Mohrlüder, J. ; Olubiyi, O. ; Strodel, B. ; Willbold, D. ; Weiergräber, O. H. (Corresponding author)
Conformational Polymorphism in Autophagy-Related Protein GATE-16
Biochemistry 54(35), 5469 - 5479 (2015) [10.1021/acs.biochem.5b00366]2015 Files BibTeX | EndNote: XML, Text | RIS

Mandler, M. ; Santic, R. ; Gruber, P. ; Cinar, Y. ; Pichler, D. ; Funke, S. A. ; Willbold, D. ; Schneeberger, A. (Corresponding Author) ; Schmidt, W. ; Mattner, F.
Tailoring the Antibody Response to Aggregated Aß Using Novel Alzheimer-Vaccines
PLoS one 10(1), e0115237 - (2015) [10.1371/journal.pone.0115237]2015 DBCoverage Files Fulltext BibTeX | EndNote: XML, Text | RIS

Medini, K. ; Harris, P. W. R. ; Hards, K. ; Dingley, A. ; Cook, G. M. ; Brimble, M. A. (Corresponding author)
Chemical synthesis of a pore-forming antimicrobial protein, caenopore-5, by using native chemical ligation at a glu-cys site.
ChemBioChem 16(2), 328 - 336 (2015) [10.1002/cbic.201402513]2015 Files BibTeX | EndNote: XML, Text | RIS

Michel, M. ; Schwarten, M. ; Decker, C. ; Nagel-Steger, L. ; Willbold, D. ; Weiergräber, O. H. (Corresponding author)
The mammalian autophagy initiator complex contains 2 HORMA domain proteins.
Autophagy 11(12), 2300 - 2308 (2015) [10.1080/15548627.2015.1076605]2015 Files BibTeX | EndNote: XML, Text | RIS

Nasica-Labouze, J. ; Nguyen, P. H. ; Sterpone, F. ; Berthoumieu, O. ; Buchete, N.-V. ; Coté, S. ; De Simone, A. ; Doig, A. J. ; Faller, P. ; Garcia, A. ; Laio, A. ; Li, M. S. ; Melchionna, S. ; Mousseau, N. ; Mu, Y. ; Paravastu, A. ; Pasquali, S. ; Rosenman, D. J. ; Strodel, B. ; Tarus, B. ; Viles, J. H. ; Zhang, T. ; Wang, C. ; Derreumaux, P. (Corresponding author)
Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies
Chemical reviews 115(9), 3518 - 3563 (2015) [10.1021/cr500638n]2015 Files BibTeX | EndNote: XML, Text | RIS

Pattky, M. ; Nicolardi, S. ; Santiago-Schübel, B. ; Sydes, D. ; van der Burgt, Y. E. M. ; Klein, A. N. ; Jiang, N. ; Mohrlüder, J. ; Hänel, K. ; Kutzsche, J. ; Funke, S. A. ; Willbold, D. ; Willbold, S. ; Huhn, C. (Corresponding author)
Structure characterization of unexpected covalent O-sulfonation and ion-pairing on an extremely hydrophilic peptide with CE-MS and FT-ICR-MS
Analytical and bioanalytical chemistry 407(22), 6637 - 6655 (2015) [10.1007/s00216-015-8826-8]2015 Files Fulltext BibTeX | EndNote: XML, Text | RIS

Petrovskaya, L. E. (Corresponding author) ; Balashov, S. P. ; Lukashev, E. P. ; Imasheva, E. S. ; Gushchin, I. ; Dioumaev, A. K. ; Rubin, A. B. ; Dolgikh, D. A. ; Gordeliy, V. ; Lanyi, J. K. ; Kirpichnikov, M. P.
ESR — A retinal protein with unusual properties from Exiguobacterium sibiricum
Biochemistry (Moscow) 80(6), 688 - 700 (2015) [10.1134/S000629791506005X]2015 Files BibTeX | EndNote: XML, Text | RIS

Sali, A. (Corresponding author) ; Berman, H. ; Schwede, T. ; Trewhella, J. ; Kleywegt, G. ; Burley, S. ; Markley, J. ; Nakamura, H. ; Adams, P. ; Bonvin, A. J. J. ; Chiu, W. ; Peraro, M. ; Di Maio, F. ; Ferrin, T. ; Grünewald, K. ; Gutmanas, A. ; Henderson, R. ; Hummer, G. ; Iwasaki, K. ; Johnson, G. ; Lawson, C. ; Meiler, J. ; Marti-Renom, M. ; Montelione, G. ; Nilges, M. ; Nussinov, R. ; Patwardhan, A. ; Rappsilber, J. ; Read, R. ; Saibil, H. ; Schröder, G. ; Schwieters, C. ; Seidel, C. M. ; Svergun, D. ; Topf, M. ; Ulrich, E. ; Velankar, S. ; Westbrook, J.
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop
Structure 23(7), 1156 - 1167 (2015) [10.1016/j.str.2015.05.013]2015 Files BibTeX | EndNote: XML, Text | RIS

Schröder, G. (Corresponding author)
Hybrid methods for macromolecular structure determination: experiment with expectations
Current opinion in structural biology 31, 20 - 27 (2015) [10.1016/j.sbi.2015.02.016]2015 Files BibTeX | EndNote: XML, Text | RIS

Shaykhalishahi, H. ; Mirecka, E. A. ; Gauhar, A. ; Grüning, C. S. R. ; Willbold, D. ; Härd, T. ; Stoldt, M. ; Hoyer, W. (Corresponding author)
A β-Hairpin-Binding Protein for Three Different Disease-Related Amyloidogenic Proteins
ChemBioChem 16(3), 411 - 414 (2015) [10.1002/cbic.201402552]2015 Files BibTeX | EndNote: XML, Text | RIS

Shaykhalishahi, H. ; Gauhar, A. ; Wördehoff, M. M. ; Grüning, C. S. R. ; Klein, A. N. ; Bannach, O. ; Stoldt, M. ; Willbold, D. ; Härd, T. ; Hoyer, W. (Corresponding author)
Contact between the β1 and β2 Segments of α-Synuclein that Inhibits Amyloid Formation
Angewandte Chemie / International edition 54(30), 8837 - 8840 (2015) [10.1002/anie.201503018]2015 Files BibTeX | EndNote: XML, Text | RIS

Sólyom, Z. ; Ma, P. ; Schwarten, M. ; Bosco, M. ; Polidori, A. ; Durand, G. ; Willbold, D. ; Brutscher, B. (Corresponding author)
The Disordered Region of the HCV Protein NS5A: Conformational Dynamics, SH3 Binding, and Phosphorylation
Biophysical journal 109(7), 1483 - 1496 (2015) [10.1016/j.bpj.2015.06.040]2015 Files BibTeX | EndNote: XML, Text | RIS

Spiegel, M. ; Duraisamy, A. K. ; Schröder, G. (Corresponding author)
Improving the visualization of cryo-EM density reconstructions
Journal of structural biology 191(2), 207 - 213 (2015) [10.1016/j.jsb.2015.06.007]2015 Files BibTeX | EndNote: XML, Text | RIS

Wildberg, A. ; Della Corte, D. ; Schröder, G. (Corresponding author)
Coupling an Ensemble of Homologues Improves Refinement of Protein Homology Models
Journal of chemical theory and computation 11(12), 5578 - 5582 (2015) [10.1021/acs.jctc.5b00942]2015 Files Fulltext BibTeX | EndNote: XML, Text | RIS

Wolff, M. ; Unuchek, D. ; Zhang, B. ; Gordeliy, V. ; Willbold, D. ; Nagel-Steger, L. (Corresponding author)
Amyloid β Oligomeric Species Present in the Lag Phase of Amyloid Formation
PLoS one 10(5), e0127865 (2015) [10.1371/journal.pone.0127865]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Wördehoff, M. M. ; Bannach, O. (Corresponding author) ; Shaykhalishahi, H. ; Kulawik, A. ; Schiefer, S. ; Willbold, D. ; Hoyer, W. ; Birkmann, E.
Single Fibril Growth Kinetics of α-Synuclein
Journal of molecular biology 427(6 B), 1428 - 1435 (2015) [10.1016/j.jmb.2015.01.020]2015 Files Fulltext BibTeX | EndNote: XML, Text | RIS

Zander, U. ; Bourenkov, G. ; Popov, A. N. ; de Sanctis, D. ; Svensson, O. ; McCarthy, A. A. ; Round, E. ; Gordeliy, V. ; Mueller-Dieckmann, C. ; Leonard, G. A. (Corresponding author)
MeshAndCollect : an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines
Acta crystallographica / D 71(11), 2328 - 2343 (2015) [10.1107/S1399004715017927]2015 Files BibTeX | EndNote: XML, Text | RIS

Last Modified: 24.01.2025