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  1. No Access

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    Advanced Crystallographic Data Collection Protocols for Experimental Phasing

    Experimental phasing by single- or multi-wavelength anomalous dispersion (SAD or MAD) has become the most popular method of de novo macromolecular structure determination. Continuous advances at third-generati...

    Aaron D. Finke, Ezequiel Panepucci, Clemens Vonrhein in Nucleic Acid Crystallography (2016)

  2. No Access

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    LC3-II Tagging and Western Blotting for Monitoring Autophagic Activity in Mammalian Cells

    The autophagosome-associated protein LC3-II is commonly used as a marker of autophagic activity within cells, but its levels are affected by both formation and degradation of autophagosomes. This can make the ...

    Anne Streeter, Fiona M. Menzies in Systems Biology of Alzheimer's Disease (2016)

  3. No Access

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    Preparation of Short 5′-Triphosphorylated Oligoribonucleotides for Crystallographic and Biochemical Studies

    RNA molecules participate in virtually all cellular processes ranging from transfer of hereditary information to gene expression control. In cells, many RNAs form specific interactions with proteins often usin...

    Nikita Vasilyev, Alexander Serganov in Nucleic Acid Crystallography (2016)

  4. No Access

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    Practical Radiation Damage-Induced Phasing

    Although crystallographers typically seek to mitigate radiation damage in macromolecular crystals, in some cases, radiation damage to specific atoms can be used to determine phases de novo. This process is cal...

    Chloe Zubieta, Max H. Nanao in Nucleic Acid Crystallography (2016)

  5. No Access

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    Yeast as a Model for Alzheimer’s Disease: Latest Studies and Advanced Strategies

    The yeast Saccharomyces cerevisiae, a unicellular eukaryotic model, has enabled major breakthroughs in our understanding of a plethora of cellular and molecular processes. Today, a ‘re-invention’ of its use in fu...

    Mathias Verduyckt, Hélène Vignaud, Tine Bynens in Systems Biology of Alzheimer's Disease (2016)

  6. No Access

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    Expression and Purification of Recombinant Cyclins and CDKs for Activity Evaluation

    Cyclin-dependent kinases (Cdks) belong to a family of key regulators of cell division cycle and transcription. Their activity is mainly regulated by association with regulatory subunits named cyclins but their...

    Edurne Gallastegui, Oriol Bachs in Cyclin-Dependent Kinase (CDK) Inhibitors (2016)

  7. No Access

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    In Vitro/In Vivo Production of tRNA for X-Ray Studies

    tRNAs occupy a central role in the cellular life, and they are involved in a broad range of biological processes that relies on their interaction with proteins and RNA. Crystallization and structure resolution...

    Clément Dégut, Alexandre Monod, Franck Brachet in Nucleic Acid Crystallography (2016)

  8. No Access

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    Using Molecular Replacement Phasing to Study the Structure and Function of RNA

    In recent years a wide variety of RNA molecules regulating fundamental cellular processes has been discovered. Therefore, RNA structure determination is experiencing a boost and many more RNA structures are li...

    Marco Marcia in Nucleic Acid Crystallography (2016)

  9. No Access

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    Drosophila melanogaster as a Model for Studies on the Early Stages of Alzheimer’s Disease

    Fruit flies (Drosophila melanogaster) have been widely used to study the cellular and molecular basis of human neurodegenerative disease. The biological similarities between the human and the fly have been explor...

    Jung Yeon Lim, Stanislav Ott, Damian C. Crowther in Systems Biology of Alzheimer's Disease (2016)

  10. No Access

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    Preparation of CDK/Cyclin Inhibitor Complexes for Structural Determination

    The abundance of biochemical and structural knowledge on the Cyclin-Dependent Kinases (CDKs) has provided a comprehensive but not exhaustive insight into the molecular determinants that govern their function m...

    Asterios I. Grigoroudis, George Kontopidis in Cyclin-Dependent Kinase (CDK) Inhibitors (2016)

  11. No Access

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    Use of the U1A Protein to Facilitate Crystallization and Structure Determination of Large RNAs

    The preparation of well-ordered crystals of RNAs with complex three-dimensional architecture can be facilitated by engineering a binding site for the spliceosomal protein U1A into a functionally and structural...

    Adrian R. Ferré-D’Amaré in Nucleic Acid Crystallography (2016)

  12. No Access

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    Homology Modeling and Docking Evaluation of Human Muscarinic Acetylcholine Receptors

    The development of GPCR homology models for virtual screening is an active area of research. Here we describe methods for homology modeling of the acetylcholine muscarinic receptors M1R–M5R. The models are based ...

    Trayder Thomas, David K. Chalmers in Muscarinic Receptor: From Structure to Ani… (2016)

  13. No Access

    Protocol

    RNA Structure Refinement Using the ERRASER-Phenix Pipeline

    The final step of RNA crystallography involves the fitting of coordinates into electron density maps. The large number of backbone atoms in RNA presents a difficult and tedious challenge, particularly when exp...

    Fang-Chieh Chou, Nathaniel Echols, Thomas C. Terwilliger in Nucleic Acid Crystallography (2016)

  14. No Access

    Protocol

    Structure of the HCV Internal Ribosome Entry Site Subdomain IIa RNA in Complex with a Viral Translation Inhibitor

    The internal ribosome entry site (IRES) in the 5′ untranslated region (UTR) of the hepatitis C virus (HCV) RNA genome is responsible for initiation of viral protein synthesis. The IRES RNA contains autonomousl...

    Sergey M. Dibrov, Thomas Hermann in Nucleic Acid Crystallography (2016)

  15. No Access

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    Gene Expression Studies on Human Trisomy 21 iPSCs and Neurons: Towards Mechanisms Underlying Down’s Syndrome and Early Alzheimer’s Disease-Like Pathologies

    The cause of Alzheimer disease (AD) is not well understood and there is no cure. Our ability to understand the early events in the course of AD is severely limited by the difficulty of identifying individuals ...

    Jason P. Weick, Huining Kang in Systems Biology of Alzheimer's Disease (2016)

  16. No Access

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    Protein-Protein Interaction for the De Novo Design of Cyclin-Dependent Kinase Peptide Inhibitors

    The homology of the inhibitor binding site regions on the surface of cyclin-dependent kinases (CDKs) makes actual CDK inhibitors unable to bind specifically to their molecular targets. Most of them are ATP com...

    Karthiga Arumugasamy, Sunil Kumar Tripathi in Cyclin-Dependent Kinase (CDK) Inhibitors (2016)

  17. No Access

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    Generating Crystallographic Models of DNA Dodecamers from Structures of RNase H:DNA Complexes

    The DNA dodecamer 5′-d(CGCGAATTCGCG)-3′ is arguably the best studied oligonucleotide and crystal structures of duplexes with this sequence account for a considerable portion of the total number of oligo-2′-deo...

    Martin Egli, Pradeep S. Pallan in Nucleic Acid Crystallography (2016)

  18. No Access

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    Binding Method for Detection of Muscarinic Acetylcholine Receptors in Receptor’s Natural Environment

    The pharmacological and biochemical properties of G protein-coupled receptors have been recently revealed to be more complex than originally supposed. Especially, in natural environment or in vivo, some recept...

    Ikunobu Muramatsu, Hatsumi Yoshiki in Muscarinic Receptor: From Structure to Ani… (2016)

  19. No Access

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    Reconstitution of Functionally Active Thermus thermophilus 30S Ribosomal Subunit from Ribosomal 16S RNA and Ribosomal Proteins

    In vitro reconstitution systems of ribosomal subunits from free ribosomal RNA and ribosomal proteins are helpful tool for studies on the structure, function and assembly of ribosome. Using this system mutant o...

    Sultan Agalarov, Marat Yusupov, Gulnara Yusupova in Nucleic Acid Crystallography (2016)

  20. No Access

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    Next Generation Sequencing in Alzheimer’s Disease

    For the first time in the history of human genetics research, it is now both technically feasible and economically affordable to screen individual genomes for novel disease-causing mutations at base-pair resol...

    Lars Bertram M.D. in Systems Biology of Alzheimer's Disease (2016)

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