{"entity": "publications", "timestamp": "2026-09-12T07:31:57.285Z", "year": "2005", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publications/2005.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publications/2005"}}, "publications_count": 9, "full": true, "publications": [{"entity": "publication", "iuid": "085bf5cb52da4eb5a5e6b446cbc21667", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/085bf5cb52da4eb5a5e6b446cbc21667.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/085bf5cb52da4eb5a5e6b446cbc21667"}}, "title": "Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis.", "authors": [{"family": "Bienko", "given": "Marzena", "initials": "M"}, {"family": "Green", "given": "Catherine M", "initials": "CM"}, {"family": "Crosetto", "given": "Nicola", "initials": "N"}, {"family": "Rudolf", "given": "Fabian", "initials": "F"}, {"family": "Zapart", "given": "Grzegorz", "initials": "G"}, {"family": "Coull", "given": "Barry", "initials": "B"}, {"family": "Kannouche", "given": "Patricia", "initials": "P"}, {"family": "Wider", "given": "Gerhard", "initials": "G"}, {"family": "Peter", "given": "Matthias", "initials": "M"}, {"family": "Lehmann", "given": "Alan R", "initials": "AR"}, {"family": "Hofmann", "given": "Kay", "initials": "K"}, {"family": "Dikic", "given": "Ivan", "initials": "I"}], "type": "journal article", "published": "2005-12-16", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "volume": "310", "issue": "5755", "pages": "1821-1824", "issn-l": "0036-8075"}, "abstract": "Translesion synthesis (TLS) is the major pathway by which mammalian cells replicate across DNA lesions. Upon DNA damage, ubiquitination of proliferating cell nuclear antigen (PCNA) induces bypass of the lesion by directing the replication machinery into the TLS pathway. Yet, how this modification is recognized and interpreted in the cell remains unclear. Here we describe the identification of two ubiquitin (Ub)-binding domains (UBM and UBZ), which are evolutionarily conserved in all Y-family TLS polymerases (pols). These domains are required for binding of poleta and poliota to ubiquitin, their accumulation in replication factories, and their interaction with monoubiquitinated PCNA. Moreover, the UBZ domain of poleta is essential to efficiently restore a normal response to ultraviolet irradiation in xeroderma pigmentosum variant (XP-V) fibroblasts. Our results indicate that Ub-binding domains of Y-family polymerases play crucial regulatory roles in TLS.", "doi": "10.1126/science.1120615", "pmid": "16357261", "labels": {"Magda Bienko": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "310/5755/1821"}], "notes": [], "created": "2020-10-05T15:01:01.969Z", "modified": "2022-11-07T11:35:11.344Z"}, {"entity": "publication", "iuid": "27ebd85d540e40369b30f6787cbc2479", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/27ebd85d540e40369b30f6787cbc2479.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/27ebd85d540e40369b30f6787cbc2479"}}, "title": "Structure of the autoinhibited kinase domain of CaMKII and SAXS analysis of the holoenzyme.", "authors": [{"family": "Rosenberg", "given": "Oren S", "initials": "OS"}, {"family": "Deindl", "given": "Sebastian", "initials": "S"}, {"family": "Sung", "given": "Rou-Jia", "initials": "RJ"}, {"family": "Nairn", "given": "Angus C", "initials": "AC"}, {"family": "Kuriyan", "given": "John", "initials": "J"}], "type": "journal article", "published": "2005-12-02", "journal": {"title": "Cell", "issn": "0092-8674", "volume": "123", "issue": "5", "pages": "849-860", "issn-l": null}, "abstract": "Ca2+/calmodulin-dependent protein kinase-II (CaMKII) is unique among protein kinases for its dodecameric assembly and its complex response to Ca2+. The crystal structure of the autoinhibited kinase domain of CaMKII, determined at 1.8 A resolution, reveals an unexpected dimeric organization in which the calmodulin-responsive regulatory segments form a coiled-coil strut that blocks peptide and ATP binding to the otherwise intrinsically active kinase domains. A threonine residue in the regulatory segment, which when phosphorylated renders CaMKII calmodulin independent, is held apart from the catalytic sites by the organization of the dimer. This ensures a strict Ca2+ dependence for initial activation. The structure of the kinase dimer, when combined with small-angle X-ray scattering data for the holoenzyme, suggests that inactive CaMKII forms tightly packed autoinhibited assemblies that convert upon activation into clusters of loosely tethered and independent kinase domains.", "doi": "10.1016/j.cell.2005.10.029", "pmid": "16325579", "labels": {"Sebastian Deindl": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S0092-8674(05)01173-6"}], "notes": [], "created": "2020-10-09T09:54:40.124Z", "modified": "2022-11-07T11:37:50.988Z"}, {"entity": "publication", "iuid": "997060dbeae04877ac9f83fb969b8d11", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/997060dbeae04877ac9f83fb969b8d11.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/997060dbeae04877ac9f83fb969b8d11"}}, "title": "Solving the structure of plant photosystem I--biochemistry is vital.", "authors": [{"family": "Amunts", "given": "Alexey", "initials": "A"}, {"family": "Ben-Shem", "given": "Adam", "initials": "A"}, {"family": "Nelson", "given": "Nathan", "initials": "N"}], "type": "journal article", "published": "2005-12-00", "journal": {"title": "Photochem. Photobiol. Sci.", "issn": "1474-9092", "volume": "4", "issue": "12", "pages": "1011-1015", "issn-l": "1474-905X"}, "abstract": "The recently determined structure of plant photosystem I (PSI) provides the first relatively high-resolution structural model of a supercomplex containing a reaction center and its peripheral antenna. Large amounts of highly purified PSI were required to get enough crystals amenable for structural determination by X-ray crystallography. In addition, a deep biochemical understanding of the large supercomplex was vital for achieving the goal. The stability of PSI was analyzed by sucrose gradient centrifugation and gel electrophoresis. Small amounts of LHCI were detached from PSI following a 12 day incubation under crystallization conditions. The interaction between the reaction center and the peripheral antenna of PSI (LHCI) as well as the interactions among the LHCI monomers are flexible. Nevertheless, the pure and homogeneous preparation of PSI allows for relatively tight crystal packing, which holds promise for obtaining atomic resolution in the future.", "doi": "10.1039/b506132f", "pmid": "16307115", "labels": {"Alexey Amunts": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-09-25T14:25:06.938Z", "modified": "2022-11-07T11:30:20.558Z"}, {"entity": "publication", "iuid": "9650fd3947704b7a9c4839951d8eac8e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9650fd3947704b7a9c4839951d8eac8e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9650fd3947704b7a9c4839951d8eac8e"}}, "title": "Biocatalysis in semi-aqueous and nearly anhydrous conditions.", "authors": [{"family": "Hudson", "given": "Elton P", "initials": "EP"}, {"family": "Eppler", "given": "Ross K", "initials": "RK"}, {"family": "Clark", "given": "Douglas S", "initials": "DS"}], "type": "journal article", "published": "2005-12-00", "journal": {"title": "Current Opinion in Biotechnology", "issn": "0958-1669", "volume": "16", "issue": "6", "pages": "637-643", "issn-l": "0958-1669"}, "abstract": "In the past few years there have been prolific advances in activating enzymes for nonaqueous biocatalysis. Molecular dynamics simulations complement recent experimental results and offer new insights into the deleterious effects of organic solvents, such as water stripping and active-site penetration. Methods for activating enzymes in semi-aqueous or nonaqueous media include protein engineering, chemical modification, and co-lyophilization with non-buffer salts. Enzyme immobilization on novel polymeric supports and the use of zeolite molecular sieves can also increase solvent tolerance, enhance activity, and improve enantioselectivity. The recent implementation of enzymes in ionic liquids has also led to better long-term stability relative to traditional organic solvents and the simultaneous solubilization of enzymes, cofactors and substrates.", "doi": "10.1016/j.copbio.2005.10.004", "pmid": "16256329", "labels": {"Paul Hudson": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S0958-1669(05)00165-5"}], "notes": [], "created": "2020-10-06T14:20:32.475Z", "modified": "2022-11-07T11:36:30.896Z"}, {"entity": "publication", "iuid": "23dafd499e534eac8f4d0a3f9f349a00", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/23dafd499e534eac8f4d0a3f9f349a00.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/23dafd499e534eac8f4d0a3f9f349a00"}}, "title": "Preparation and evaluation of (68)Ga-DOTA-hEGF for visualization of EGFR expression in malignant tumors.", "authors": [{"family": "Velikyan", "given": "Irina", "initials": "I", "orcid": "0000-0002-3732-8857", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/947ae561cd794e5b94c6736880620287.json"}}, {"family": "Sundberg", "given": "Asa Liljegren", "initials": "AL"}, {"family": "Lindhe", "given": "Orjan", "initials": "O"}, {"family": "H\u00f6glund", "given": "A Urban", "initials": "AU"}, {"family": "Eriksson", "given": "Olof", "initials": "O", "orcid": "0000-0002-2515-8790", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/85991bf00e4b4a26ab15599d25c58601.json"}}, {"family": "Werner", "given": "Eva", "initials": "E"}, {"family": "Carlsson", "given": "Jorgen", "initials": "J", "orcid": "0000-0003-4623-2977", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/792c1cd4aca248dc94b967115ffa82df.json"}}, {"family": "Bergstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "L\u00e5ngstr\u00f6m", "given": "Bengt", "initials": "B"}, {"family": "Tolmachev", "given": "Vladimir", "initials": "V"}], "type": "evaluation study", "published": "2005-11-00", "journal": {"title": "Journal of nuclear medicine : official publication, Society of Nuclear Medicine", "issn": "0161-5505", "volume": "46", "issue": "11", "pages": "1881-1888", "issn-l": null}, "abstract": "Detection of epidermal growth factor receptor (EGFR) overexpression in many carcinomas provides important diagnostic information, which can influence patient management. The use of PET may enable such detection in vivo by a noninvasive procedure with high sensitivity. The aim of this study was to develop a method for preparation of a positron-emitting tracer based on a natural ligand to EGFR, the recombinant human epidermal growth factor (hEGF), and to perform a preclinical evaluation of the tracer.\n\nDOTA-hEGF (DOTA is 1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid) was prepared by coupling of a N-sulfosuccinimide ester of DOTA to hEGF. The conjugate was labeled with a generator-produced positron-emitting nuclide, (68)Ga (half-life = 68 min), using microwave heating. Binding specificity, affinity, internalization, and retention of (68)Ga-DOTA-hEGF was studied in 2 EGFR-expressing cell lines, U343 glioma cells and A431 cervical carcinoma cells. Biodistribution and microPET visualization studies were performed in BALB/c nu/nu mice bearing A431 carcinoma xenografts.\n\nA 1-min-long microwave-assisted labeling provided radioactivity incorporation of 77% +/- 4%. Both cell lines demonstrated receptor-specific uptake of the conjugate, rapid internalization of the tracer, and good retention of radioactivity. Binding to both cell lines occurred with high affinity, approximately 2 nmol/L. The biodistribution study demonstrated accumulation of radioactivity in xenografts and in EGFR-expressing organs. The microPET imaging study enabled visualization of tumors and demonstrated quick--within 5 min--localization of radioactivity in tumors.\n\n(68)Ga-DOTA-hEGF has potential for imaging EGFR overexpression in tumors.", "doi": null, "pmid": "16269603", "labels": {"Olof Eriksson": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "46/11/1881"}], "notes": [], "created": "2020-10-06T14:12:38.035Z", "modified": "2025-11-17T09:14:34.656Z"}, {"entity": "publication", "iuid": "b99f7a8faefe416598a172834b3d869c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b99f7a8faefe416598a172834b3d869c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b99f7a8faefe416598a172834b3d869c"}}, "title": "Isolation of novel single-chain Cro proteins targeted for binding to the bcl-2 transcription initiation site by repertoire selection and subunit combinatorics.", "authors": [{"family": "Jonas", "given": "Kristina", "initials": "K"}, {"family": "Van Der Vries", "given": "Erhard", "initials": "E"}, {"family": "Nilsson", "given": "Mikael T I", "initials": "MT"}, {"family": "Widersten", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2005-11-00", "journal": {"title": "Protein Eng. Des. Sel.", "issn": "1741-0126", "volume": "18", "issue": "11", "pages": "537-546", "issn-l": null}, "abstract": "New designed DNA-binding proteins may be recruited to act as transcriptional regulators and could provide new therapeutic agents in the treatment of genetic disorders such as cancer. We have isolated tailored DNA-binding proteins selected for affinity to a region spanning the transcription initiation site of the human bcl-2 gene. The proteins were derived from a single-chain derivative of the lambda Cro protein (scCro), randomly mutated in its recognition helices to construct libraries of protein variants of distinct DNA-binding properties. By phage display-afforded affinity selections combined with recombination of shuffled subunits, protein variants were isolated, which displayed high affinity for the target bcl-2 sequence, as determined by electrophoretic mobility shift and biosensor assays. The proteins analyzed were moderately sequence-specific but provide a starting point for further maturation of desired function.", "doi": "10.1093/protein/gzi058", "pmid": "16186141", "labels": {"Kristina Jonas": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "gzi058"}], "notes": [], "created": "2020-11-30T14:49:04.554Z", "modified": "2022-11-07T11:33:47.354Z"}, {"entity": "publication", "iuid": "b9d5a83d1e47446f9145d30501f41259", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b9d5a83d1e47446f9145d30501f41259.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b9d5a83d1e47446f9145d30501f41259"}}, "title": "Two-photon activation and excitation properties of PA-GFP in the 720-920-nm region.", "authors": [{"family": "Schneider", "given": "Marc", "initials": "M"}, {"family": "Barozzi", "given": "Sara", "initials": "S"}, {"family": "Testa", "given": "Ilaria", "initials": "I"}, {"family": "Faretta", "given": "Mario", "initials": "M"}, {"family": "Diaspro", "given": "Alberto", "initials": "A"}], "type": "evaluation study", "published": "2005-08-00", "journal": {"title": "Biophysical Journal", "issn": "0006-3495", "volume": "89", "issue": "2", "pages": "1346-1352", "issn-l": "0006-3495"}, "abstract": "This report covers the two-photon activation and excitation properties of the PA-GFP, a photoactivatable variant of the Aequorea victoria green fluorescent protein in the spectral region from 720 to 920 nm. It is known from this special form of the molecule that it has an increased level of fluorescence emission when excited at 488 nm after irradiation at lambda approximately 413 nm, under single-photon excitation conditions. Here, we show that upon two-photon irradiation, PA-GFP yields activation in the spectral region from 720 to 840 nm. After photoactivation, the excitation spectrum shifts maintaining the very same emission spectrum of the single-photon case for the native and photoactivated protein. Additionally, when comparing the conventional photoactivation at lambda = 405 nm with a two-photon one, a sharper and better controllable three-dimensional volume of activation is obtained.", "doi": "10.1529/biophysj.104.054502", "pmid": "15908572", "labels": {"Ilaria Testa": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S0006-3495(05)72782-X"}, {"db": "pmc", "key": "PMC1366619"}], "notes": [], "created": "2020-09-29T13:07:37.982Z", "modified": "2022-11-07T11:32:31.842Z"}, {"entity": "publication", "iuid": "316b39ef6bd444e8a2512baa95a5fef9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/316b39ef6bd444e8a2512baa95a5fef9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/316b39ef6bd444e8a2512baa95a5fef9"}}, "title": "Flame-coating of titania particles with silica", "authors": [{"family": "Teleki", "given": "A", "initials": "A"}, {"family": "Pratsinis", "given": "S E", "initials": "SE"}, {"family": "Wegner", "given": "K", "initials": "K"}, {"family": "Jossen", "given": "R", "initials": "R"}, {"family": "Krumeich", "given": "F", "initials": "F"}], "type": "journal-article", "published": "2005-05-00", "journal": {"title": "J. Mater. Res.", "issn": "0884-2914", "volume": "20", "issue": "5", "pages": "1336-1347", "issn-l": null}, "abstract": null, "doi": "10.1557/jmr.2005.0160", "pmid": null, "labels": {"Alexandra Teleki": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-11-30T21:52:38.919Z", "modified": "2022-11-07T11:29:43.777Z"}, {"entity": "publication", "iuid": "04866739d6744eb799918d433ee76485", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/04866739d6744eb799918d433ee76485.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/04866739d6744eb799918d433ee76485"}}, "title": "Absolute and relative entropies from computer simulation with applications to ligand binding.", "authors": [{"family": "Carlsson", "given": "Jens", "initials": "J"}, {"family": "Aqvist", "given": "Johan", "initials": "J"}], "type": "comparative study", "published": "2005-04-07", "journal": {"title": "J. Phys. Chem. B", "issn": "1520-6106", "volume": "109", "issue": "13", "pages": "6448-6456", "issn-l": "1520-5207"}, "abstract": "A comparison between two related methods, Schlitter's formula and quasiharmonic analysis, for calculating absolute entropies from the covariance matrix of atomic fluctuations using molecular dynamics (MD) simulations is presented. Calculations for a set of organic compounds in the gas phase are compared to the corresponding statistical thermodynamics results for translational and rotational entropies and to experimental data for vibrational entropies. Encouraging agreement is obtained for translational entropies, but for the rotational contribution, both methods fail to reproduce the theoretically calculated values. Absolute and relative vibrational entropies are found to be better reproduced using quasiharmonic analysis compared to Schlitter's formula. For rotational entropies, we propose a method based on the variances in Euler angles, which gives good agreement with theory. Alternative methods for estimating translational entropies based on principal root mean-square (rms) fluctuations of the center of mass are also presented, and these reproduce theoretically calculated values well. These methodologies are applied to the binding of benzene to T4-lysozyme, where close agreement with the literature is obtained for translational and rotational entropies.", "doi": "10.1021/jp046022f", "pmid": "16851719", "labels": {"Jens Carlsson": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-09-29T13:52:15.861Z", "modified": "2022-11-07T11:33:17.822Z"}]}