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1. Full Text Restricted leucine zipper dimerization and specificity of DNA recognition of the melanocyte master regulator MITF
by Pogenberg, Vivian and Ögmundsdóttir, Margrét H and Bergsteinsdóttir, Kristín and Schepsky, Alexander and Phung, Bengt and Deineko, Viktor and Milewski, Morlin and Steingrímsson, Eiríkur and Wilmanns, Matthias and Lund University and Lunds universitet and Institutionen för translationell medicin and Department of Translational Medicine
Genes and Development, ISSN 0890-9369, 12/2012, Volume 26, Issue 23, pp. 2647 - 2658
Microphthalmia-associated transcription factor (MITF) is a master regulator of melanocyte development and an important oncogene in melanoma. MITF heterodimeric... 
Leucine zipper | Transcription factor | Melanocyte regulation | DNA binding | Crystal structure | transcription factor | melanocyte regulation | COMPLEX | PREDISPOSES | PROTEIN | MAX | CRYSTAL-STRUCTURE | PROLIFERATION | MECHANISMS | DEVELOPMENTAL BIOLOGY | CELL BIOLOGY | MICROPHTHALMIA TRANSCRIPTION FACTOR | leucine zipper | MUTATION | GENETICS & HEREDITY | crystal structure | EXPRESSION | Protein Structure, Tertiary | Amino Acid Sequence | Microphthalmia-Associated Transcription Factor - metabolism | Microphthalmia-Associated Transcription Factor - chemistry | Humans | Models, Molecular | Molecular Sequence Data | DNA-Binding Proteins - genetics | DNA-Binding Proteins - chemistry | Leucine Zippers - genetics | DNA-Binding Proteins - metabolism | Sequence Alignment | Animals | Waardenburg Syndrome - genetics | Protein Binding | Enhancer Elements, Genetic - genetics | Mice | Mutation | Dimerization | Microphthalmia-Associated Transcription Factor - genetics | Transcription factors | Genetic disorders | Physiological aspects | Melanocytes | Genetic aspects | Research | Structure | Properties | Health aspects | Protein binding | Research Paper | leucine | Genetik | Biological Sciences | Naturvetenskap | zipper | Genetics | Biologi | Natural Sciences
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2. Full Text Protein-DNA binding in the absence of specific base-pair recognition
by Ariel Afek and Joshua L. Schipper and John Horton and Raluca Gordân and David B. Lukatsky
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 12/2014, Volume 111, Issue 48, pp. 17140 - 17145
Until now, it has been reasonably assumed that specific base-pair recognition is the only mechanism controlling the specificity of transcription factor... 
Transcription factors | DNA | Genomics | Correlations | Nucleotide sequences | Experiment design | Statistical mechanics | Free energy | Binding sites | Symmetry | Protein-DNA binding | Nonspecific protein-DNA binding | Transcriptional regulation | TRANSCRIPTION FACTORS | transcriptional regulation | STABILITY | MULTIDISCIPLINARY SCIENCES | GENOME | protein-DNA binding | SHAPE | OPERATOR | nonspecific protein-DNA binding | LAC REPRESSOR | SITES | MICROARRAYS | SELECTION | FACILITATED TARGET LOCATION | Protein Structure, Tertiary | Repetitive Sequences, Nucleic Acid - genetics | Transcription Factors - chemistry | Nucleotide Motifs - genetics | Humans | Models, Molecular | Binding Sites - genetics | DNA - metabolism | Transcription Factors - genetics | DNA-Binding Proteins - genetics | DNA-Binding Proteins - chemistry | Sequence Homology, Nucleic Acid | DNA - genetics | DNA-Binding Proteins - metabolism | Transcription Factors - metabolism | Thermodynamics | DNA - chemistry | Algorithms | Base Pairing | Base Sequence | Protein Binding | Nucleic Acid Conformation | High-Throughput Screening Assays - methods | Protein research | Research | DNA-ligand interactions | Protein binding | protein−DNA binding | Biological Sciences | nonspecific protein−DNA binding
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3. Full Text The Mre11:Rad50 Structure Shows an ATP-Dependent Molecular Clamp in DNA Double-Strand Break Repair
by Lammens, Katja and Bemeleit, Derk J and Möckel, Carolin and Clausing, Emanuel and Schele, Alexandra and Hartung, Sophia and Schiller, Christian B and Lucas, Maria and Angermüller, Christof and Söding, Johannes and Sträßer, Katja and Hopfner, Karl-Peter
Cell, ISSN 0092-8674, 04/2011, Volume 145, Issue 1, pp. 54 - 66
The MR (Mre11 nuclease and Rad50 ABC ATPase) complex is an evolutionarily conserved sensor for DNA double-strand breaks, highly genotoxic lesions linked to... 
KINASE-ACTIVITY | RECOMBINATION | CHROMOSOME | DAMAGE RESPONSE | RAD50 | MRE11 COMPLEX | SBCCD | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | MECHANISMS | PROTEIN COMPLEX | CELL BIOLOGY | Bacterial Proteins - chemistry | DNA Repair Enzymes - genetics | Crystallography, X-Ray | DNA Breaks, Double-Stranded | DNA-Binding Proteins - metabolism | X-Ray Diffraction | Adenosine Triphosphate - metabolism | DNA Repair Enzymes - metabolism | Endodeoxyribonucleases - metabolism | Thermotoga maritima - chemistry | Thermotoga maritima - metabolism | DNA Repair Enzymes - chemistry | Bacterial Proteins - genetics | Models, Molecular | Scattering, Small Angle | Endodeoxyribonucleases - chemistry | DNA-Binding Proteins - genetics | DNA-Binding Proteins - chemistry | Saccharomyces cerevisiae - chemistry | DNA Repair | Exodeoxyribonucleases - metabolism | Saccharomyces cerevisiae Proteins - metabolism | Bacterial Proteins - metabolism | Exodeoxyribonucleases - chemistry | Saccharomyces cerevisiae Proteins - chemistry | X-ray crystallography | Rad50 | DNA double-strand break repair | Mre11 | homologous recombination | protein complex | ABC ATPases
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4. Full Text Analysis and prediction of single-stranded and double-stranded DNA binding proteins based on protein sequences
by Wang, Wei and Sun, Lin and Zhang, Shiguang and Zhang, Hongjun and Shi, Jinling and Xu, Tianhe and Li, Keliang
BMC Bioinformatics, ISSN 1471-2105, 06/2017, Volume 18, Issue 1, pp. 300 - 10
Background: DNA-binding proteins perform important functions in a great number of biological activities. DNA-binding proteins can interact with ssDNA... 
SSBs (Single-stranded DNA-binding proteins) | Protein sequence | DSBs (Double-stranded DNA-binding proteins) | Binding specificity | EVOLUTIONARY | RECOGNITION | SPECIFICITY | BIOCHEMICAL RESEARCH METHODS | SUBCELLULAR-LOCALIZATION | IDENTIFICATION | FEATURES | INTERFACE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | SITES | OB-FOLD | DOMAINS | DNA-Binding Proteins - metabolism | Amino Acid Sequence | Sequence Analysis, Protein - methods | Computational Biology - methods | DNA, Single-Stranded - metabolism | Protein Binding | DNA - metabolism | Support Vector Machine | DNA-Binding Proteins - genetics | DNA-Binding Proteins - chemistry | Amino acids | DNA binding proteins | Analysis | DNA | Protein binding | Single-stranded DNA | Nucleotide sequence | Amino acid composition | Scoring | Gene expression | Gene sequencing | Genetic algorithms | Datasets | Proteins | Support vector machines | DNA-binding protein | Acids | Single-stranded DNA-binding protein | International conferences | Localization | Bioinformatics | Binding sites | Deoxyribonucleic acid--DNA | Methods
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5. Full Text DNA ligase III promotes alternative nonhomologous end-joining during chromosomal translocation formation
by Simsek, Deniz and Brunet, Erika and Wong, Sunnie Yan-Wai and Katyal, Sachin and Gao, Yankun and McKinnon, Peter J and Lou, Jacqueline and Zhang, Lei and Li, James and Rebar, Edward J and Gregory, Philip D and Holmes, Michael C and Jasin, Maria
PLoS Genetics, ISSN 1553-7390, 06/2011, Volume 7, Issue 6, p. e1002080
Nonhomologous end-joining (NHEJ) is the primary DNA repair pathway thought to underlie chromosomal translocations and other genomic rearrangements in somatic... 
PATHWAYS | RECOMBINATION | REPAIR | GENETICS & HEREDITY | DOUBLE-STRAND BREAKS | POLY(ADP-RIBOSE) POLYMERASE-1 | GENE AMPLIFICATION | COMPONENT | REARRANGEMENTS | ZINC-FINGER NUCLEASES | MAMMALIAN-CELLS | Translocation, Genetic | DNA Ligases - genetics | Molecular Sequence Data | Xenopus Proteins | DNA-Binding Proteins - genetics | DNA Ligases - metabolism | DNA-Binding Proteins - metabolism | Poly-ADP-Ribose Binding Proteins | Animals | Cell Nucleus - metabolism | Transfection | Base Sequence | DNA Repair | DNA Ligase ATP | Mice | Models, Genetic | Physiological aspects | Research | DNA binding proteins | Translocation (Genetics) | Ligases | DNA Ligases | Life Sciences | Genetics | Cell Nucleus | DNA-Binding Proteins | Proteins | DNA repair | Chromosomes
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6. Full Text TALE nucleases: tailored genome engineering made easy
by Mussolino, Claudio and Cathomen, Toni
Current Opinion in Biotechnology, ISSN 0958-1669, 2012, Volume 23, Issue 5, pp. 644 - 650
Graphical abstract TALEN-mediated genome engineering. After a TALEN pair has cleaved the target locus, the resulting DNA double strand break will be repaired... 
Internal Medicine | III EFFECTORS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | EMBRYONIC STEM-CELLS | MAJOR DETERMINANT | BIOCHEMICAL RESEARCH METHODS | DOUBLE-STRAND BREAKS | EFFECTOR NUCLEASES | HOMOLOGOUS RECOMBINATION | CLEAVAGE | ZINC-FINGER NUCLEASES | KNOCKOUT RATS | DNA-BINDING SPECIFICITY | Genetic Engineering - methods | Protein Structure, Tertiary | Endonucleases - genetics | Zinc Fingers | Humans | Transcriptional Activation | Genome - genetics | Endonucleases - metabolism | DNA-Binding Proteins - genetics | Stem Cells - metabolism | DNA-Binding Proteins - chemistry | Endonucleases - chemistry | DNA-Binding Proteins - metabolism | Animals | Nucleases | Genomics | DNA binding proteins
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7. Full Text Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX
by Ko, Myunggon and An, Jungeun and Bandukwala, Hozefa S and Chavez, Lukas and Äijö, Tarmo and Pastor, William A and Segal, Matthew F and Li, Huiming and Koh, Kian Peng and Lähdesmäki, Harri and Hogan, Patrick G and Aravind, L and Rao, Anjana
Nature, ISSN 0028-0836, 2013, Volume 497, Issue 7447, pp. 122 - 126
TET (ten-eleven-translocation) proteins are Fe(II)- and alpha-ketogluta-rate-dependent dioxygenases(1-3) that modify the methylation status of DNA by... 
WNT SIGNALING PATHWAY | COMPLEX | DNA METHYLATION | MAMMALIAN DNA | MULTIDISCIPLINARY SCIENCES | EMBRYONIC STEM-CELLS | 5-HYDROXYMETHYLCYTOSINE CONTENT | DIFFERENTIATION | BINDING PROTEIN | CPG ISLANDS | 5-CARBOXYLCYTOSINE | Embryonic Stem Cells - metabolism | Dioxygenases - metabolism | Transcription Factors - chemistry | Humans | Transcription Factors - deficiency | Proto-Oncogene Proteins - chemistry | Proto-Oncogene Proteins - biosynthesis | Promoter Regions, Genetic - genetics | DNA-Binding Proteins - deficiency | DNA-Binding Proteins - metabolism | Caspases - metabolism | U937 Cells | Base Sequence | HEK293 Cells | Protein Interaction Domains and Motifs | Protein Structure, Tertiary | Proto-Oncogene Proteins - metabolism | Catalytic Domain | Dioxygenases - chemistry | Oxidation-Reduction | Down-Regulation | Proto-Oncogene Proteins - genetics | DNA Methylation - genetics | Transcription Factors - genetics | DNA-Binding Proteins - genetics | DNA-Binding Proteins - chemistry | Transcription Factors - metabolism | Animals | Dioxygenases - genetics | 5-Methylcytosine - metabolism | CpG Islands - genetics | Mice | Enzyme Activation | DNA-Binding Proteins - biosynthesis | Physiological aspects | Oxidation-reduction reaction | Cytosine | Genetic aspects | Research | Gene expression | Methylation | Proteins | Enzymes | Oxidation | Rodents | Cytoplasm
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8. Full Text Foxp3 programs the development and function of CD4 + CD25 + regulatory T cells
by Rudensky, Alexander Y and Gavin, Marc A and Fontenot, Jason D
Nature Immunology, ISSN 1529-2908, 04/2003, Volume 4, Issue 4, pp. 330 - 336
CD4(+)CD25(+) regulatory T cells are essential for the active suppression of autoimmunity. Here we report that the forkhead transcription factor Foxp3 is... 
INTESTINAL INFLAMMATION | HOMEOSTASIS | ENTEROPATHY | POSITIVE SELECTION | AUTOIMMUNITY | TOLERANCE | MICE | IL-2 | SCURFY MOUSE MUTANT | SF MOUSE | IMMUNOLOGY | Gene Targeting | DNA-Binding Proteins - immunology | Down-Regulation | CD4-Positive T-Lymphocytes - metabolism | Receptors, Interleukin-2 - metabolism | DNA-Binding Proteins - genetics | Receptors, Interleukin-2 - immunology | CD4-Positive T-Lymphocytes - immunology | DNA-Binding Proteins - metabolism | Animals | Female | Mice | Forkhead Transcription Factors
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9. Full Text A Yeast TDP-43 Proteinopathy Model: Exploring the Molecular Determinants of TDP-43 Aggregation and Cellular Toxicity
by Brian S. Johnson and J. Michael McCaffery and Susan Lindquist and Aaron D. Gitler
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 4/2008, Volume 105, Issue 17, pp. 6439 - 6444
Protein misfolding is intimately associated with devastating human neurodegenerative diseases, including Alzheimer's, Huntington's, and Parkinson's. Although... 
Aggregation | Proteins | Yeasts | Pathology | Nervous system diseases | Neurodegenerative diseases | Neurons | Parkinson disease | Cell aggregates | Alzheimers disease | Frontal temporal dementia | Amyotrophic lateral sclerosis | Saccharomyces cerevisiae | TAR-DNA-binding protein | DNA-Binding Proteins - metabolism | Saccharomyces cerevisiae - cytology | Cell Nucleus - metabolism | Peptides - metabolism | Amyloid - metabolism | Models, Biological | Protein Structure, Quaternary | Inclusion Bodies - metabolism | DNA-Binding Proteins - chemistry | Protein Transport | Protein folding | Cell death | Influence | Research | DNA binding proteins | Properties | Cytoplasm | Index Medicus | Biological Sciences | frontal temporal dementia | amyotrophic lateral sclerosis | TAR–DNA-binding protein
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10. Full Text CENP-T-W-S-X Forms a Unique Centromeric Chromatin Structure with a Histone-like Fold
by Nishino, Tatsuya and Takeuchi, Kozo and Gascoigne, Karen E and Suzuki, Aussie and Hori, Tetsuya and Oyama, Takuji and Morikawa, Kosuke and Cheeseman, Iain M and Fukagawa, Tatsuo
Cell, ISSN 0092-8674, 02/2012, Volume 148, Issue 3, pp. 487 - 501
The multiprotein kinetochore complex must assemble at a specific site on each chromosome to achieve accurate chromosome segregation. Defining the nature of the... 
CORE | COMPLEX | CRYSTAL-STRUCTURE | DNA | BIOCHEMISTRY & MOLECULAR BIOLOGY | NUCLEOSOME | CELL BIOLOGY | Protein Structure, Tertiary | Amino Acid Sequence | Chromatin - metabolism | Chromosomal Proteins, Non-Histone - metabolism | Kinetochores - metabolism | Humans | Models, Molecular | Molecular Sequence Data | Centromere - metabolism | DNA-Binding Proteins - genetics | DNA-Binding Proteins - chemistry | Chromosomal Proteins, Non-Histone - genetics | Centromere - chemistry | Chickens - metabolism | DNA-Binding Proteins - metabolism | Animals | X-Ray Diffraction | Histones - metabolism | Mutation | Chromosomal Proteins, Non-Histone - chemistry | Kinetochores - chemistry | Chromatin - chemistry | Chromatin | Molecular genetics | Analysis | Histones | DNA binding proteins | DNA-ligand interactions | The X-ray Structure | Kinetochore | CENP-T-W | CENP-S-X | DNA binding
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