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4. Ensemble-based characterization of unbound and bound states on protein energy landscape

Author

Ruvinsky, Anatoly M., Kirys, Tatsiana, Tuzikov, Alexander V., and Vakser, Ilya A.

Subjects
Physics - Biological Physics, Quantitative Biology - Biomolecules
Abstract

Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their binding mechanisms and characterize the energy landscapes in implicit solvent. First, results show that bound and unbound spectra often significantly overlap. Moreover, the larger the overlap the smaller the RMSD between bound and unbound conformational ensembles. Second, the analysis of the unbound-to-bound changes points to conformational selection as the binding mechanism for four of the proteins. Third, the center of the unbound spectrum has a higher energy than the center of the corresponding bound spectrum of the dimeric and multimeric states for most of the proteins. This suggests that the unbound states often have larger entropy than the bound states considered outside of the complex. Fourth, the exhaustively long minimization, making small intra-rotamer adjustments, dramatically reduces the distance between the centers of the bound and unbound spectra as well as the spectra extent. It condenses unbound and bound energy levels into a thin layer at the bottom of the energy landscape with the energy spacing that varies between 0.8-4.6 and 3.5-10.5 kcal/mol for the unbound and bound states correspondingly. At the same time, the energy gap between the two lowest states in the full ensemble varies between 0.9 and 12.1 kcal/mol. Finally, the analysis of protein energy fluctuations showed that protein vibrations itself can excite the inter-state transitions, thus supporting the conformational selection theory., Comment: 12 pages, 5 figures, 2 tables, supporting material

Published
2012

5. Structure fluctuations and conformational changes in protein binding

Author

Ruvinsky, Anatoly M., Kirys, Tatsiana, Tuzikov, Alexander V., and Vakser, Ilya A.

Subjects
Physics - Biological Physics, Quantitative Biology - Biomolecules
Abstract

Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers of mass in proteins and a statistical analysis of conformation changes in the side-chains upon binding. Normal mode analysis and an elastic network model were applied to a set of protein complexes to calculate the residue fluctuations and develop the residue classification. Comparison with a classification based on normalized B-factors suggests that the B-factors may underestimate protein flexibility in solvent. Our classification shows that protein loops and disordered fragments are enriched with highly fluctuating residues and depleted with weakly fluctuating residues. To calculate the dihedral angles distribution functions, the configuration space was divided into cells by a cubic grid. The effect of protein association on the distribution functions depends on the amino acid type and a grid step in the dihedral angles space. The changes in the dihedral angles increase from the near-backbone dihedral angle to the most distant one, for most residues. On average, one fifth of the interface residues change the rotamer state upon binding, whereas the rest of the interface residues undergo local readjustments within the same rotamer., Comment: 13 pages, 6 figures

Published
2011
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6. Side-chain conformational changes upon protein-protein association

Author

Ruvinsky, Anatoly M., Kirys, Tatsiana, Tuzikov, Alexander V., and Vakser, Ilya A.

Subjects
Quantitative Biology - Biomolecules, Physics - Biological Physics
Abstract

Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short and long side chains have different propensities for the conformational changes. Long side chains with three or more dihedral angles are often subject to large conformational transition. Shorter residues with one or two dihedral angles typically undergo local conformational changes not leading to a conformational transition. The relationship between the local readjustments and the equilibrium fluctuations of a side chain around its unbound conformation is suggested. Most of the side chains undergo larger changes in the dihedral angle most distant from the backbone. The amino acids with symmetric aromatic (Phe and Tyr) and charged (Asp and Glu) groups show the opposite trend where the near-backbone dihedral angles change the most. The frequencies of the core-to-surface interface transitions of six nonpolar residues and Tyr exceed the frequencies of the opposite, surface-to-core transitions. The binding increases both polar and nonpolar interface areas. However, the increase of the nonpolar area is larger for all considered classes of protein complexes. The results suggest that the protein association perturbs the unbound interfaces to increase the hydrophobic forces. The results facilitate better understanding of the conformational changes in proteins and suggest directions for efficient conformational sampling in docking protocols., Comment: 21 pages, 6 figures

Published
2010

7. Labeling of Polysaccharides with Biotin and Fluorescent Dyes.

Author

Tuzikov, Alexander, Shilova, Nadezhda, Ovchinnikova, Tatiana, Nokel, Alexey, Patova, Olga, Knirel, Yuriy, Chernova, Tatiana, Gorshkova, Tatiana, and Bovin, Nicolai

Subjects
*POLYSACCHARIDES, *BIOTIN, *FLUORESCEIN isothiocyanate, *CARBOXYL group, *HYALURONIC acid, *GLYCOLIPIDS, *FLUORESCENT dyes
Abstract

Examples of labeling polysaccharides at hydroxyl groups are described in this paper, which are especially in demand for molecules with a blocked reducing end. The protocols presented are suitable for the microscale synthesis of labeled polysaccharides that do not require a chromatography step for isolation. Examples of hydroxyl labeling include (1) direct modification with fluorescein isothiocyanate; (2) reaction with a fluorescein-dichlorotriazine derivative; (3) reaction with biotin-dichlorotriazine; (4) indirect two-step modification (given for glycosphingolipid) with glutaric anhydride followed by amidation with aminospacered BODIPY or SuCy5. The labeling of carboxyl groups of hyaluronic acid with BODIPY is also described. The staining of plant tissue sections with biotinylated polysaccharide versus being fluorescein labeled is compared. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Poly-L-Lysine-Based αGal-Glycoconjugates for Treating Anti-αGal IgE-Mediated Diseases

Author

Olivera-Ardid, Sara, Bello-Gil, Daniel, Tuzikov, Alexander, Araujo, Ricardo N., Ferrero-Alves, Yara, García Figueroa, Blanca Esther, Labrador Horrillo, Moises, García-Pérez, Ana L., Bovin, Nicolai, Mañez, Rafael, Universitat Autònoma de Barcelona. Departament de Medicina, Institut Català de la Salut, [Olivera-Ardid S, Bello-Gil D, Ferrero-Alves Y] RemAb Therapeutics, Mòdul de Recerca B, Universitat Autònoma de Barcelona, Bellaterra, Spain. [Tuzikov A] Department of Chemical Biology of Glycans and Lipids, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia. [Araujo RN] Laboratório de Artrópodes Hematófagos, Departamento de Parasitologia, ICB/UFMG, Belo Horizonte, Brazil. [García Figueroa BE] MEGA: Asthma Inception and Progression Mechanisms, Complejo Hospitalario de Navarra (CHN), Pamplona, Spain. Instituto de investigación sanitaria de Navarra (IdiSNA), Pamplona, Spain. ARADyAL Research Network, Instituto de Salud Carlos III (ISCIII), Madrid, Spain. [Labrador-Horrillo M] ARADyAL Research Network, Instituto de Salud Carlos III (ISCIII), Madrid, Spain. Departament de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain. Secció d’Al•lèrgia, Servei de Medicina Interna, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Àrea de Malalties Immunomediades i Teràpies Innovadores, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain, and Vall d'Hebron Barcelona Hospital Campus

Subjects
Al·lèrgia, Allergy, Immunology, Immunoteràpia, αGal-syndrome, Immunotheraphy, Poly-l-lysine-based αGal-glycoconjugates, Mice, Immunology and Allergy, Animals, Humans, Polylysine, Ratolins, Eukaryota::Animals::Chordata::Vertebrates::Mammals::Eutheria::Rodentia::Muridae::Murinae::Mice [ORGANISMS], hidratos de carbono::glicoconjugados [COMPUESTOS QUÍMICOS Y DROGAS], Immune System Diseases::Hypersensitivity::Hypersensitivity, Immediate::Food Hypersensitivity [DISEASES], GalT-KO mice, Anti-αgal IgE inhibition, Immunoglobulin E, Carbohydrates::Glycoconjugates [CHEMICALS AND DRUGS], Al·lèrgia alimentària, Immunoglobulin M, Glicoconjugats, Immunoglobulin G, Immunotherapy, Eukaryota::animales::Chordata::vertebrados::mamíferos::Eutheria::Rodentia::Muridae::Murinae::ratones [ORGANISMOS], Glycoconjugates, Food Hypersensitivity, enfermedades del sistema inmune::hipersensibilidad::hipersensibilidad inmediata::hipersensibilidad a los alimentos [ENFERMEDADES]
Abstract

Anti-αGal IgE antibodies mediate a spreading allergic condition known as αGal-syndrome (AGS). People exposed to hard tick bites are sensitized to αGal, producing elevated levels of anti-αGal IgE, which are responsible for AGS. This work presents an immunotherapy based on polymeric αGal-glycoconjugates for potentially treating allergic disorders by selectively inhibiting anti-αGal IgE antibodies. We synthesized a set of αGal-glycoconjugates, based on poly-L-lysine of different degrees of polymerization (DP1000, DP600, and DP100), to specifically inhibit in vitro the anti-αGal IgE antibodies in the serum of αGal-sensitized patients (n=13). Moreover, an animal model for αGal sensitization in GalT-KO mice was developed by intradermal administration of hard tick’ salivary gland extract, mimicking the sensitization mechanism postulated in humans. The in vitro exposure to all polymeric glycoconjugates (5-10-20-50-100 µg/mL) mainly inhibited anti-αGal IgE and IgM isotypes, with a lower inhibition effect on the IgA and IgG, respectively. We demonstrated a differential anti-αGal isotype inhibition as a function of the length of the poly-L-lysine and the number of αGal residues exposed in the glycoconjugates. These results defined a minimum of 27 αGal residues to inhibit most of the induced anti-αGal IgE in vitro. Furthermore, the αGal-glycoconjugate DP1000-RA0118 (10 mg/kg sc.) showed a high capacity to remove the anti-αGal IgE antibodies (≥75% on average) induced in GalT-KO mice, together with similar inhibition for circulating anti-αGal IgG and IgM. Our study suggests the potential clinical use of poly-L-lysine-based αGal-glycoconjugates for treating allergic disorders mediated by anti-αGal IgE antibodies. Copyright © 2022 Olivera-Ardid, Bello-Gil, Tuzikov, Araujo, Ferrero-Alves, García Figueroa, Labrador-Horrillo, García-Pérez, Bovin and Mañez.

Published
2022

14. Lipopolysaccharide From E. coli Increases Glutamate-Induced Disturbances of Calcium Homeostasis, the Functional State of Mitochondria, and the Death of Cultured Cortical Neurons

Author

Bakaeva, Zanda, primary, Lizunova, Natalia, additional, Tarzhanov, Ivan, additional, Boyarkin, Dmitrii, additional, Petrichuk, Svetlana, additional, Pinelis, Vsevolod, additional, Fisenko, Andrey, additional, Tuzikov, Alexander, additional, Sharipov, Rinat, additional, and Surin, Alexander, additional

Published
2022
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16. Localization of synthetic glycolipids in the cell and the dynamics of their insertion/loss

Author

Rapoport, Eugenia M., primary, Khasbiullina, Nailya R., additional, Komarova, Veronika A., additional, Ryzhov, Ivan M., additional, Gorbatch, Mikhail M., additional, Tuzikov, Alexander B., additional, Khaidukov, Sergey V., additional, Popova, Inna S., additional, Korchagina, Elena Y., additional, Henry, Stephen M., additional, and Bovin, Nicolai V., additional

Published
2021
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18. Moment computation for objects with spline curve boundary

Author

Sheynin, Stanislav and Tuzikov, Alexander

Subjects
Machine vision -- Research
Abstract

A new approach is proposed for computation of area and geometric moments for a plane object with a spline curve boundary. The explicit formulae are obtained for area and low order moment calculation. The complexity of calculation depends on the moment order, spline degree, and the number of control points used in spline representation. The formulae proposed use the advantage that the sequence of spline control points is cyclic. It allowed us to reduce substantially the number of summands in them. The formulae might be useful in different applications where it is necessary to perform measurements for shapes with a smooth boundary. Index Terms--Area, moment, parametric curve, spline, explicit formulae.

Published
2003

20. Structure of Supramers Formed by the Amphiphile Biotin‐CMG‐DOPE

Author

Zalygin, Anton, primary, Solovyeva, Daria, additional, Vaskan, Ivan, additional, Henry, Stephen, additional, Schaefer, Marcel, additional, Volynsky, Pavel, additional, Tuzikov, Alexander, additional, Korchagina, Elena, additional, Ryzhov, Ivan, additional, Nizovtsev, Alexey, additional, Mochalov, Konstantin, additional, Efremov, Roman, additional, Shtykova, Eleonora, additional, Oleinikov, Vladimir, additional, and Bovin, Nicolai, additional

Published
2020
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22. Similarity and symmetry measures for convex shapes using Minkowski addition

Author

Heijmans, Henk J.A.M. and Tuzikov, Alexander V.

Subjects
Convex domains -- Measurement, Symmetry -- Analysis, Pattern recognition -- Research, Similarity (Geometry) -- Analysis
Abstract

This paper is devoted to similarity and symmetry measures for convex shapes whose definition is based on Minkowski addition and the Brunn-Minkowski inequality. This means, in particular, that these measures are region-based, in contrast to most of the literature, where one considers contour-based measures. All measures considered in this paper are invariant under translations; furthermore, they can be chosen to be invariant under rotations, multiplications, reflections, or the class of affine transformations. It is shown that the mixed volume of a convex polygon and a rotation of another convex polygon over an angle [Theta] is a piecewise concave function of [Theta]. This and other results of a similar nature form the basis for the development of efficient algorithms for the computation of the given measures. Various results obtained in this paper are illustrated by experimental data. Although the paper deals exclusively with the two-dimensional case, many of the theoretical results carry over almost directly to higher-dimensional spaces. Index Terms - Similarity measure, symmetry measure, convex set, Minkowski addition, Brunn-Minkowski inequality.

Published
1998

25. Correlation analysis of the side-chains conformational distribution in bound and unbound proteins

Author

Kirys Tatsiana, Ruvinsky Anatoly M, Tuzikov Alexander V, and Vakser Ilya A

Subjects
Protein interactions, Protein docking, Molecular recognition, Conformational analysis, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Protein interactions play a key role in life processes. Characterization of conformational properties of protein-protein interactions is important for understanding the mechanisms of protein association. The rapidly increasing amount of experimentally determined structures of proteins and protein-protein complexes provides foundation for research on protein interactions and complex formation. The knowledge of the conformations of the surface side chains is essential for modeling of protein complexes. The purpose of this study was to analyze and compare dihedral angle distribution functions of the side chains at the interface and non-interface areas in bound and unbound proteins. Results To calculate the dihedral angle distribution functions, the configuration space was divided into grid cells. Statistical analysis showed that the similarity between bound and unbound interface and non-interface surface depends on the amino acid type and the grid resolution. The correlation coefficients between the distribution functions increased with the grid spacing increase for all amino acid types. The Manhattan distance showing the degree of dissimilarity between the distribution functions decreased accordingly. Short residues with one or two dihedral angles had higher correlations and smaller Manhattan distances than the longer residues. Met and Arg had the slowest growth of the correlation coefficient with the grid spacing increase. The correlations between the interface and non-interface distribution functions had a similar dependence on the grid resolution in both bound and unbound states. The interface and non-interface differences between bound and unbound distribution functions, caused by biological protein-protein interactions or crystal contacts, disappeared at the 70° grid spacing for interfaces and 30° for non-interface surface, which agrees with an average span of the side-chain rotamers. Conclusions The two-fold difference in the critical grid spacing indicates larger conformational changes upon binding at the interface than at the rest of the surface. At the same time, transitions between rotamers induced by interactions across the interface or the crystal packing are rare, with most side chains having local readjustments that do not change the rotameric state. The analysis is important for better understanding of protein interactions and development of flexible docking approaches.

Published
2012
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27. 6-sulfo sialyl Lewis X is the common receptor determinant recognized by H5, H6, H7 and H9 influenza viruses of terrestrial poultry

Author

Bovin Nicolai V, Desheva Julia A, Pazynina Galina V, Tuzikov Alexander B, Gambaryan Alexandra S, Matrosovich Mikhail N, and Klimov Alexander I

Subjects
Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Influenza A viruses of domestic birds originate from the natural reservoir in aquatic birds as a result of interspecies transmission and adaptation to new host species. We previously noticed that influenza viruses isolated from distinct orders of aquatic and terrestrial birds may differ in their fine receptor-binding specificity by recognizing the structure of the inner parts of Neu5Acα2-3Gal-terminated sialyloligosaccharide receptors. To further characterize these differences, we studied receptor-binding properties of a large panel of influenza A viruses from wild aquatic birds, poultry, pigs and horses. Results Using a competitive solid-phase binding assay, we determined viral binding to polymeric conjugates of sialyloligosaccharides differing by the type of Neu5Acα-Gal linkage and by the structure of the more distant parts of the oligosaccharide chain. Influenza viruses isolated from terrestrial poultry differed from duck viruses by an enhanced binding to sulfated and/or fucosylated Neu5Acα2-3Gal-containing sialyloligosaccharides. Most of the poultry viruses tested shared a high binding affinity for the 6-sulfo sialyl Lewis X (Su-SLex). Efficient binding of poultry viruses to Su-SLex was often accompanied by their ability to bind to Neu5Acα2-6Gal-terminated (human-type) receptors. Such a dual receptor-binding specificity was demonstrated for the North American and Eurasian H7 viruses, H9N2 Eurasian poultry viruses, and H1, H3 and H9 avian-like virus isolates from pigs. Conclusion Influenza viruses of terrestrial poultry differ from ancestral duck viruses by enhanced binding to sulfated and/or fucosylated Neu5Acα2-3Gal-terminated receptors and, occasionally, by the ability to bind to Neu5Acα2-6Gal-terminated (human-type) receptors. These findings suggest that the adaptation to receptors in poultry can enhance the potential of an avian virus for avian-to-human transmission and pandemic spread.

Published
2008
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28. Structural motifs in protein cores and at protein–protein interfaces are different.

Author

Hadarovich, Anna, Chakravarty, Devlina, Tuzikov, Alexander V., Ben‐Tal, Nir, Kundrotas, Petras J., and Vakser, Ilya A.

Abstract

Structures of proteins and protein–protein complexes are determined by the same physical principles and thus share a number of similarities. At the same time, there could be differences because in order to function, proteins interact with other molecules, undergo conformations changes, and so forth, which might impose different restraints on the tertiary versus quaternary structures. This study focuses on structural properties of protein–protein interfaces in comparison with the protein core, based on the wealth of currently available structural data and new structure‐based approaches. The results showed that physicochemical characteristics, such as amino acid composition, residue–residue contact preferences, and hydrophilicity/hydrophobicity distributions, are similar in protein core and protein–protein interfaces. On the other hand, characteristics that reflect the evolutionary pressure, such as structural composition and packing, are largely different. The results provide important insight into fundamental properties of protein structure and function. At the same time, the results contribute to better understanding of the ways to dock proteins. Recent progress in predicting structures of individual proteins follows the advancement of deep learning techniques and new approaches to residue coevolution data. Protein core could potentially provide large amounts of data for application of the deep learning to docking. However, our results showed that the core motifs are significantly different from those at protein–protein interfaces, and thus may not be directly useful for docking. At the same time, such difference may help to overcome a major obstacle in application of the coevolutionary data to docking—discrimination of the intramolecular information not directly relevant to docking. [ABSTRACT FROM AUTHOR]

Published
2021
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29. Receptor-binding properties of influenza viruses isolated from gulls

Author

Gambaryan, Alexandra S., primary, Matrosovich, Tatyana Y., additional, Boravleva, Elisaveta Y., additional, Lomakina, Natalia F., additional, Yamnikova, Svetlana S., additional, Tuzikov, Alexander B., additional, Pazynina, Galina V., additional, Bovin, Nicolai V., additional, Fouchier, Ron A.M., additional, Klenk, Hans-Dieter, additional, and Matrosovich, Mikhail N., additional

Published
2018
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31. The TB Portals: an Open-Access, Web-Based Platform for Global Drug-Resistant-Tuberculosis Data Sharing and Analysis

Author

Rosenthal, Alex, primary, Gabrielian, Andrei, additional, Engle, Eric, additional, Hurt, Darrell E., additional, Alexandru, Sofia, additional, Crudu, Valeriu, additional, Sergueev, Eugene, additional, Kirichenko, Valery, additional, Lapitskii, Vladzimir, additional, Snezhko, Eduard, additional, Kovalev, Vassili, additional, Astrovko, Andrei, additional, Skrahina, Alena, additional, Taaffe, Jessica, additional, Harris, Michael, additional, Long, Alyssa, additional, Wollenberg, Kurt, additional, Akhundova, Irada, additional, Ismayilova, Sharafat, additional, Skrahin, Aliaksandr, additional, Mammadbayov, Elcan, additional, Gadirova, Hagigat, additional, Abuzarov, Rafik, additional, Seyfaddinova, Mehriban, additional, Avaliani, Zaza, additional, Strambu, Irina, additional, Zaharia, Dragos, additional, Muntean, Alexandru, additional, Ghita, Eugenia, additional, Bogdan, Miron, additional, Mindru, Roxana, additional, Spinu, Victor, additional, Sora, Alexandra, additional, Ene, Catalina, additional, Vashakidze, Sergo, additional, Shubladze, Natalia, additional, Nanava, Ucha, additional, Tuzikov, Alexander, additional, and Tartakovsky, Michael, additional

Published
2017
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33. PESI - a taxonomic backbone for Europe

Author

de Jong, Yde, Kouwenberg, Juliana, Boumans, Louis, Hussey, Charles, Hyam, Roger, Nicolson, Nicola, Kirk, Paul, Paton, Alan, Michel, Ellinor, Guiry, Michael, Boegh, Phillip, Pedersen, Henrik Ærenlund, Enghoff, Henrik, von Raab-Straube, Eckhard, Güntsch, Anton, Geoffroy, Marc, Müller, Andreas, Kohlbecker, Andreas, Berendsohn, Walter, Appeltans, Ward, Arvanitidis, Christos, Vanhoorne, Bart, Declerck, Joram, Vandepitte, Leen, Hernandez, Francisco, Nash, Róisín, Costello, Mark, Ouvrard, David, Bezard-Falgas, Pascale, Bourgoin, Thierry, Wetzel, Florian, Glöckler, Falko, Korb, Günther, Ring, Caroline, Hagedorn, Gregor, Häuser, Christoph, Aktaç, Nihat, Asan, Ahmet, Ardelean, Adorian, Borges, Paulo, Dhora, Dhimiter, Khachatryan, Hasmik, Malicky, Michael, Ibrahimov, Shaig, Tuzikov, Alexander, De Wever, Aaike, Moncheva, Snejana, Spassov, Nikolai, Chobot, Karel, Popov, Alexi, Boršić, Igor, Sfenthourakis, Spyros, Kõljalg, Urmas, Uotila, Pertti, Olivier, Gargominy, Dauvin, Jean-Claude, Tarkhnishvili, David, Chaladze, Giorgi, Tuerkay, Michael, Legakis, Anastasios, Peregovits, László, Gudmundsson, Gudmundur, Ólafsson, Erling, Lysaght, Liam, Galil, Bella, Raimondo, Francesco, Domina, Gianniantonio, Stoch, Fabio, Minelli, Alessandro, Spungis, Voldermars, Budrys, Eduardas, Olenin, Sergej, Turpel, Armand, Walisch, Tania, Krpach, Vladimir, Gambin, Marie, Ungureanu, Laurentia, Karaman, Gordan, Kleukers, Roy, Stur, Elisabeth, Aagaard, Kaare, Valland, Nils, Moen, Toril, Bogdanowicz, Wieslaw, Tykarski, Piotr, Węsławski, Jan, Kędra, Monika, M. de Frias Martins, Antonio, Abreu, António, Silva, Ricardo, Medvedev, Sergei, Ryss, Alexander, Šimić, Smiljka, Marhold, Karol, Stloukal, Eduard, Tome, Davorin, Ramos, Marian, Valdés, Benito, Pina, Francisco, Kullander, Sven, Telenius, Anders, Gonseth, Yves, Tschudin, Pascal, Sergeyeva, Oleksandra, Vladymyrov, Volodymyr, Rizun, Volodymyr, Raper, Chris, Lear, Dan, Stoev, Pavel, Penev, Lyubomir, Rubio, Ana, Backeljau, Thierry, Saarenmaa, Hannu, Ulenberg, Sandrine, de Jong, Yde, Kouwenberg, Juliana, Boumans, Louis, Hussey, Charles, Hyam, Roger, Nicolson, Nicola, Kirk, Paul, Paton, Alan, Michel, Ellinor, Guiry, Michael, Boegh, Phillip, Pedersen, Henrik Ærenlund, Enghoff, Henrik, von Raab-Straube, Eckhard, Güntsch, Anton, Geoffroy, Marc, Müller, Andreas, Kohlbecker, Andreas, Berendsohn, Walter, Appeltans, Ward, Arvanitidis, Christos, Vanhoorne, Bart, Declerck, Joram, Vandepitte, Leen, Hernandez, Francisco, Nash, Róisín, Costello, Mark, Ouvrard, David, Bezard-Falgas, Pascale, Bourgoin, Thierry, Wetzel, Florian, Glöckler, Falko, Korb, Günther, Ring, Caroline, Hagedorn, Gregor, Häuser, Christoph, Aktaç, Nihat, Asan, Ahmet, Ardelean, Adorian, Borges, Paulo, Dhora, Dhimiter, Khachatryan, Hasmik, Malicky, Michael, Ibrahimov, Shaig, Tuzikov, Alexander, De Wever, Aaike, Moncheva, Snejana, Spassov, Nikolai, Chobot, Karel, Popov, Alexi, Boršić, Igor, Sfenthourakis, Spyros, Kõljalg, Urmas, Uotila, Pertti, Olivier, Gargominy, Dauvin, Jean-Claude, Tarkhnishvili, David, Chaladze, Giorgi, Tuerkay, Michael, Legakis, Anastasios, Peregovits, László, Gudmundsson, Gudmundur, Ólafsson, Erling, Lysaght, Liam, Galil, Bella, Raimondo, Francesco, Domina, Gianniantonio, Stoch, Fabio, Minelli, Alessandro, Spungis, Voldermars, Budrys, Eduardas, Olenin, Sergej, Turpel, Armand, Walisch, Tania, Krpach, Vladimir, Gambin, Marie, Ungureanu, Laurentia, Karaman, Gordan, Kleukers, Roy, Stur, Elisabeth, Aagaard, Kaare, Valland, Nils, Moen, Toril, Bogdanowicz, Wieslaw, Tykarski, Piotr, Węsławski, Jan, Kędra, Monika, M. de Frias Martins, Antonio, Abreu, António, Silva, Ricardo, Medvedev, Sergei, Ryss, Alexander, Šimić, Smiljka, Marhold, Karol, Stloukal, Eduard, Tome, Davorin, Ramos, Marian, Valdés, Benito, Pina, Francisco, Kullander, Sven, Telenius, Anders, Gonseth, Yves, Tschudin, Pascal, Sergeyeva, Oleksandra, Vladymyrov, Volodymyr, Rizun, Volodymyr, Raper, Chris, Lear, Dan, Stoev, Pavel, Penev, Lyubomir, Rubio, Ana, Backeljau, Thierry, Saarenmaa, Hannu, and Ulenberg, Sandrine

Published
2015

34. Protein models: The Grand Challenge of protein docking

Author

Anishchenko, Ivan, Kundrotas, Petras J., Tuzikov, Alexander V., and Vakser, Ilya A.

Subjects
Molecular Docking Simulation, Binding Sites, Molecular Sequence Data, Protein Interaction Mapping, Proteins, Amino Acid Sequence, Reference Standards, Article, Protein Structure, Secondary, Software, Protein Structure, Tertiary
Abstract

Characterization of life processes at the molecular level requires structural details of protein–protein interactions (PPIs). The number of experimentally determined protein structures accounts only for a fraction of known proteins. This gap has to be bridged by modeling, typically using experimentally determined structures as templates to model related proteins. The fraction of experimentally determined PPI structures is even smaller than that for the individual proteins, due to a larger number of interactions than the number of individual proteins, and a greater difficulty of crystallizing protein–protein complexes. The approaches to structural modeling of PPI (docking) often have to rely on modeled structures of the interactors, especially in the case of large PPI networks. Structures of modeled proteins are typically less accurate than the ones determined by X-ray crystallography or nuclear magnetic resonance. Thus the utility of approaches to dock these structures should be assessed by thorough benchmarking, specifically designed for protein models. To be credible, such benchmarking has to be based on carefully curated sets of structures with levels of distortion typical for modeled proteins. This article presents such a suite of models built for the benchmark set of the X-ray structures from the Dockground resource (http://dockground.bioinformatics.ku.edu) by a combination of homology modeling and Nudged Elastic Band method. For each monomer, six models were generated with predefined Cα root mean square deviation from the native structure (1, 2, . . ., 6 Å). The sets and the accompanying data provide a comprehensive resource for the development of docking methodology for modeled proteins.

Published
2013

35. Measures and indices of reflection symmetry for convex polyhedra

Author

Tuzikov, Alexander V., Roerdink, J B T M, Heijmans, H J A M, Tuzikov, Alexander V., Roerdink, Jos B.T.M., Heijmans, Henk J.A.M., Sheynin, Stanislav V., Tuzikov, Alexander V., Roerdink, J B T M, Heijmans, H J A M, Tuzikov, Alexander V., Roerdink, Jos B.T.M., Heijmans, Henk J.A.M., and Sheynin, Stanislav V.

Abstract

This paper discusses measures of reflection symmetry for 3D convex sets which are based on Minkowski addition and Brunn-Minkowski inequalities for volume and mixed volume. These measures are invariant to similitude transformations. It is also shown how these measures can be computed efficiently for convex polyhedra.

Published
1998

36. Molecular Modeling of Structural Complexes of Glycosphingolipids With the HIV-1 GP120 V3 Loop as a Framework for the Development of Anti-Aids Drugs of a New Generation

Author

Anishchenko, Ivan V., Andrianov, Alexander M., and Tuzikov, Alexander V.

Abstract

A sctructural complex of -galactosylceramide with the HIV-1 V3 loop peptides that imitate the most probable binding site for glycolipids was generated by molecular docking simulations. Based on the analysis of this complex, two water soluble analogs of -galactosylceramide, which should preserve a high affinity to V3 characteristic of the native molecule, were designed and their anti-HIV-1 activity was predicted by free energy calculations. In the light of the findings obtained, the simulated glycolipids may be considered as the promising basic structures for the development of novel potent antiviral agents that target (block) the envelope gp120 V3 loop.

Published
2011

37. PESI - a taxonomic backbone for Europe

Author

de Jong, Yde, primary, Kouwenberg, Juliana, additional, Boumans, Louis, additional, Hussey, Charles, additional, Hyam, Roger, additional, Nicolson, Nicola, additional, Kirk, Paul, additional, Paton, Alan, additional, Michel, Ellinor, additional, Guiry, Michael, additional, Boegh, Phillip, additional, Pedersen, Henrik, additional, Enghoff, Henrik, additional, von Raab-Straube, Eckhard, additional, Güntsch, Anton, additional, Geoffroy, Marc, additional, Müller, Andreas, additional, Kohlbecker, Andreas, additional, Berendsohn, Walter, additional, Appeltans, Ward, additional, Arvanitidis, Christos, additional, Vanhoorne, Bart, additional, Declerck, Joram, additional, Vandepitte, Leen, additional, Hernandez, Francisco, additional, Nash, Róisín, additional, Costello, Mark, additional, Ouvrard, David, additional, Bezard-Falgas, Pascale, additional, Bourgoin, Thierry, additional, Wetzel, Florian, additional, Glöckler, Falko, additional, Korb, Günther, additional, Ring, Caroline, additional, Hagedorn, Gregor, additional, Häuser, Christoph, additional, Aktaç, Nihat, additional, Asan, Ahmet, additional, Ardelean, Adorian, additional, Borges, Paulo, additional, Dhora, Dhimiter, additional, Khachatryan, Hasmik, additional, Malicky, Michael, additional, Ibrahimov, Shaig, additional, Tuzikov, Alexander, additional, De Wever, Aaike, additional, Moncheva, Snejana, additional, Spassov, Nikolai, additional, Chobot, Karel, additional, Popov, Alexi, additional, Boršić, Igor, additional, Sfenthourakis, Spyros, additional, Kõljalg, Urmas, additional, Uotila, Pertti, additional, Olivier, Gargominy, additional, Dauvin, Jean-Claude, additional, Tarkhnishvili, David, additional, Chaladze, Giorgi, additional, Tuerkay, Michael, additional, Legakis, Anastasios, additional, Peregovits, László, additional, Gudmundsson, Gudmundur, additional, Ólafsson, Erling, additional, Lysaght, Liam, additional, Galil, Bella, additional, Raimondo, Francesco, additional, Domina, Gianniantonio, additional, Stoch, Fabio, additional, Minelli, Alessandro, additional, Spungis, Voldermars, additional, Budrys, Eduardas, additional, Olenin, Sergej, additional, Turpel, Armand, additional, Walisch, Tania, additional, Krpach, Vladimir, additional, Gambin, Marie, additional, Ungureanu, Laurentia, additional, Karaman, Gordan, additional, Kleukers, Roy, additional, Stur, Elisabeth, additional, Aagaard, Kaare, additional, Valland, Nils, additional, Moen, Toril, additional, Bogdanowicz, Wieslaw, additional, Tykarski, Piotr, additional, Węsławski, Jan, additional, Kędra, Monika, additional, M. de Frias Martins, Antonio, additional, Abreu, António, additional, Silva, Ricardo, additional, Medvedev, Sergei, additional, Ryss, Alexander, additional, Šimić, Smiljka, additional, Marhold, Karol, additional, Stloukal, Eduard, additional, Tome, Davorin, additional, Ramos, Marian, additional, Valdés, Benito, additional, Pina, Francisco, additional, Kullander, Sven, additional, Telenius, Anders, additional, Gonseth, Yves, additional, Tschudin, Pascal, additional, Sergeyeva, Oleksandra, additional, Vladymyrov, Volodymyr, additional, Rizun, Volodymyr, additional, Raper, Chris, additional, Lear, Dan, additional, Stoev, Pavel, additional, Penev, Lyubomir, additional, Rubio, Ana, additional, Backeljau, Thierry, additional, Saarenmaa, Hannu, additional, and Ulenberg, Sandrine, additional

Published
2015
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48. Measures and indices of reflection symmetry for convex polyhedra

Author

Roerdink, J B T M, Heijmans, H J A M, Tuzikov, Alexander V., Roerdink, Jos B.T.M., Heijmans, Henk J.A.M., Sheynin, Stanislav V., Roerdink, J B T M, Heijmans, H J A M, Tuzikov, Alexander V., Roerdink, Jos B.T.M., Heijmans, Henk J.A.M., and Sheynin, Stanislav V.

Abstract

This paper discusses measures of reflection symmetry for 3D convex sets which are based on Minkowski addition and Brunn-Minkowski inequalities for volume and mixed volume. These measures are invariant to similitude transformations. It is also shown how these measures can be computed efficiently for convex polyhedra.

Published
1998

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