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      Lysine Methylation as a Routine Rescue Strategy for Protein Crystallization

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          Summary

          Crystallization remains a critical step in X-ray structure determination. Because it is not generally possible to rationally predict crystallization conditions, commercial screens have been developed which sample a wide range of crystallization space. While this approach has proved successful in many cases, a significant number of proteins fail to crystallize despite being soluble and monodispersed. It is established that chemical modification can facilitate the crystallization of otherwise intractable proteins. Here we describe a method for the reductive methylation of lysine residues which is simple, inexpensive, and efficient, and report on its application to ten proteins. We describe the effect of methylation on the physico-chemical properties of these proteins, and show that it led to diffraction-quality crystals from four proteins and structures for three that had hitherto proved refractory to crystallization. The method is suited to both low- and high-throughput laboratories.

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          Most cited references35

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          RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins.

          Recent studies have found many proteins containing regions that do not form well-defined three-dimensional structures in their native states. The study and detection of such disordered regions is important both for understanding protein function and for facilitating structural analysis since disordered regions may affect solubility and/or crystallizability. We have developed the regional order neural network (RONN) software as an application of our recently developed 'bio-basis function neural network' pattern recognition algorithm to the detection of natively disordered regions in proteins. The results of blind-testing a panel of nine disorder prediction tools (including RONN) against 80 protein sequences derived from the Protein Data Bank shows that, based on the probability excess measure, RONN performed the best.
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            An RNA cap (nucleoside-2'-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization.

            Viruses represent an attractive system with which to study the molecular basis of mRNA capping and its relation to the RNA transcription machinery. The RNA-dependent RNA polymerase NS5 of flaviviruses presents a characteristic motif of S-adenosyl-L-methionine-dependent methyltransferases at its N-terminus, and polymerase motifs at its C-terminus. The crystal structure of an N-terminal fragment of Dengue virus type 2 NS5 is reported at 2.4 A resolution. We show that this NS5 domain includes a typical methyltransferase core and exhibits a (nucleoside-2'-O-)-methyltransferase activity on capped RNA. The structure of a ternary complex comprising S-adenosyl-L-homocysteine and a guanosine triphosphate (GTP) analogue shows that 54 amino acids N-terminal to the core provide a novel GTP-binding site that selects guanine using a previously unreported mechanism. Binding studies using GTP- and RNA cap-analogues, as well as the spatial arrangement of the methyltransferase active site relative to the GTP-binding site, suggest that the latter is a specific cap-binding site. As RNA capping is an essential viral function, these results provide a structural basis for the rational design of drugs against the emerging flaviviruses.
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              Structure at 2.8 A resolution of cytochrome c oxidase from Paracoccus denitrificans.

              The crystal structure at 2.8 A resolution of the four protein subunits containing cytochrome c oxidase from the soil bacterium Paracoccus denitrificans, complexed with antibody Fv fragment, is described. Subunit I contains 12 membrane-spanning, primarily helical segments and binds haem a and the haem a3-copper B binuclear centre where molecular oxygen is reduced to water. Two proton transfer pathways, one for protons consumed in water formation and one for 'proton pumping', could be identified. Mechanisms for proton pumping are discussed.
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                Author and article information

                Contributors
                Journal
                Structure
                Structure
                Structure (London, England : 1993)
                Elsevier Ltd.
                0969-2126
                1878-4186
                14 November 2006
                November 2006
                14 November 2006
                : 14
                : 11
                : 1617-1622
                Affiliations
                [1 ]Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
                [2 ]Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
                Author notes
                []Corresponding author jonathan@ 123456strubi.ox.ac.uk
                [3]

                Lab address: http://www.oppf.ox.ac.uk

                [4]

                Lab address: http://www.strubi.ox.ac.uk

                Article
                S0969-2126(06)00391-1
                10.1016/j.str.2006.09.005
                7126202
                17098187
                ef8a8076-6a78-4b76-b3e8-2f81cc57a426
                Copyright © 2006 Elsevier Ltd. All rights reserved.

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

                History
                : 8 August 2006
                : 28 August 2006
                : 1 September 2006
                Categories
                Article

                Molecular biology
                Molecular biology

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