http://www.mdpi.com/journal/ijms/special_issues/protein_crystallography/ Dear Colleagues, In the last decades, X-Ray Diffraction Crystallography emerged as a powerful tool in the study of proteins and other macromolecules at the molecular and atomic levels. According to the Protein Data Bank, approximately 85% of the known protein structures and complexes were determined using crystallographic techniques. It is a fundamental tool to obtain crucial information in Structural Biology and related areas as structure-based drug discovery and design. The combined use of Crystallography and other methods have also shown to be of great help in the understanding of biochemical processes in the living cell. The special issue “Protein Crystallography” of IJMS covers this important research area. Dr. Ricardo Aparicio Guest Editor Additional Instructions for Authors publishing in the special issue "Protein Crystallography" All of the contributions should be oriented towards biological macromolecules. Data quality should be clearly stated in all cases. Authors are encouraged to follow international standards when publishing structural data. To ensure data deposition and availability for the scientific community, authors of structural communications should follow the guidelines for the deposition and release of macromolecular coordinate and experimental data of the International Union of Crystallography Commission on Biological Macromolecules (Acta Crystallogr. D Biol. Crystallogr. 2000, 56, 2). Coordinates and structure factors must be deposited in the Protein Data Bank and reference codes should be supplied before the paper publication. Leading Papers and Reviews Dauter, Z. Current state and prospects of macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 2006, 62, 1-11. (Review Article) Blundell, T. L.; Sibanda, B. L.; Montalvao, R. W.; Brewerton, S.; Chelliah, V.; Worth, C. L.; Harmer, N. J.; Davies, O.; Burke, D. Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2006, 361, 413-423. (Review Article) Blundell, T. L.; Patel, S. High-throughput X-ray crystallography for drug discovery. Curr. Opin. Pharmacol. 2004, 4, 490-496. (Review Article) Bahar, M.; Ballard, C.; Cohen, S. X.; Cowtan, K. D.; Dodson, E. J.; Emsley, P.; Esnouf, R. M.; Keegan, R.; Lamzin, V.; Langer, G.; Levdikov, V.; Long, F.; Meier, C.; Muller, A.; Murshudov G. N.; Perrakis, A.; Siebold, C.; Stein, N.; Turkenburg, M. G.; Vagin, A. A.; Winn, M.; Winter, G.; Wilson, K. S. SPINE workshop on automated X-ray analysis: a progress report. Acta Crystallogr. D Biol. Crystallogr. 2006, 62, 1170-1183. (Review Article) Davis, A. M.; Teague, S. J.; Kleywegt, G. J. Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew. Chem. Int. Ed. Engl. 2003, 42, 2718-2736. (Review Article) Kleywegt, G. J.; Jones, T. A. Homo crystallographicus - quo vadis? Structure 2002, 10, 465-472. Dauter, Z.; Dauter, M.; Dodson, E. Jolly SAD. Acta Crystallogr. D Biol. Crystallogr. 2002, 58, 494-506. EU 3-D Validation Network. Who checks the checkers? Four validation tools applied to eight atomic resolution structures. J. Mol. Biol. 1998, 276, 417-436. Russell, R. B.; Alber, F.; Aloy, P.; Davis, F. P.; Korkin, D.; Pichaud, M.; Topf, M.; Sali A. A structural perspective on protein-protein interactions. Curr. Opin. Struct. Biol. 2004, 14, 313-324. (Review Article) Sorensen, T. L.; McAuley, K. E.; Flaig, R.; Duke, E. M. New light for science: synchrotron radiation in structural medicine. Trends Biotechnol. 2006, 24, 500-8. (Review Article) Lundstrom, K. Structural genomics for membrane proteins. Cell. Mol. Life Sci. 2006, 63, 2597-607. (Review Article) Sali, A.; Glaeser, R.; Earnest, T.; Baumeister, W. From words to literature in structural proteomics. Nature 2003, 422, 216-225. (Review Article) Chiu, W.; Baker, M. L.; Almo, S. C. Structural biology of cellular machines. Trends Cell Biol. 2006, 16, 144-150. (Review Article) Liljas, A. On the complementarity of methods in structural biology. Acta Crystallogr. D Biol. Crystallogr. 2006, 62, 941-945. (Review Article) Koch, M. H. J.; Vachette, P.; Svergun, D. I. Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q. Rev. Biophys. 2003, 36, 147-227. (Review Article) Grossmann, J. G. Biological solution scattering: recent achievements and future challenges. J. Appl. Crystallogr. 2007, 40, S217-S222. Geerlof, A.; Brown, J.; Coutard, B.; Egloff, M. P.; Enguita, F. J.; Fogg, M. J.; Gilbert, R. J.; Groves, M. R.; Haouz, A.; Nettleship, J. E.; Nordlund, P.; Owens, R. J.; Ruff, M.; Sainsbury, S.; Svergun, D. I.; Wilmanns, M. The impact of protein characterization in structural proteomics. Acta Crystallogr. D Biol. Crystallogr. 2006, 62, 1125-36. (Review Article) Submission All papers should be submitted to ijms@mdpi.org. To be published continuously until the deadline and papers will be listed together at the special issue website. Submitted papers should not have been published previously, nor be under consideration for publication elsewhere. All papers are refereed through a peer-review process. A guide for authors is available on the Instructions for Authors page. The International Journal of Molecular Sciences is an international peer-reviewed monthly journal published by Molecular Diversity Preservation International. Open Access publication fees are 800 CHF per paper. English correction fees and/or formatting fees (250 CHF) will be added in certain cases (1050 CHF per paper for those papers that require extensive additional formatting and/or English corrections). http://www.mdpi.com/1422-0067/9/7/1131/ Hydrolysis is an often-encountered obstacle in the crystallization of proteins complexed with their substrates. As the duration of the crystallization process, from nucleation to the growth of the crystal to its final size, commonly requires several weeks, non-enzymatic hydrolysis of an “unstable” ligand occurs frequently. In cases where the crystallization conditions exhibit non neutral pH values this hydrolysis phenomenon may be even more pronounced. ChoX, the substrate binding protein of a choline ABC-importer, produced crystals with its substrate acetylcholine after one month. However, these crystals exhibited only choline, an acetylcholine hydrolysis product, in the binding site. To overcome this obstacle we devised a microseeding protocol leading to crystals of ChoX with bound acetylcholine within 24 hours. One drawback we encountered was the high twinning fraction of the crystals, possibly was due to the rapid crystal growth. http://www.mdpi.com/1422-0067/9/7/1131/ Tue, 08 Jul 2008 00:00:00 CEST International Journal of Molecular Sciences 2008-07-08 9 7 Article 1131 1141 1422-0067 Microseeding – A Powerful Tool for Crystallizing Proteins Complexed with Hydrolyzable Substrates 2008-07-08 doi: 10.3390/ijms9071131 Christine Oswald Sander H. J. Smits Erhard Bremer Lutz Schmitt http://www.mdpi.com/1422-0067/9/6/943/ Through alternative promoter usage, human retinoblastoma protein-interacting zinc finger gene RIZ encodes two different protein products, RIZ1 and RIZ2, which have been identified to be a tumor suppressor and a proto-oncoprotein, respectively. Structurally, the two protein products share the same amino acid sequences except that RIZ2 lacks an N-terminal PR domain with methyltransferase activity. Previous studies have shown that over-expression of RIZ2 is usually associated with depressed RIZ1 expression in different human cancers. It is generally believed that RIZ1 and RIZ2 regulate normal cell division and function using a “Yin-Yang” fashion and the PR domain is responsible for the tumor suppressing activity of RIZ1. In order to better understand the biological functions of the PR domain by determining its three-dimensional crystal structure, we expressed, purified and crystallized a construct of the PR domain (amino acid residues 13-190) in this study. The maximum size of the needle-shaped crystals was approximately 0.20 x 0.01 x 0.01 mm. http://www.mdpi.com/1422-0067/9/6/943/ Mon, 02 Jun 2008 00:00:00 CEST International Journal of Molecular Sciences 2008-06-02 9 6 Article 943 950 1422-0067 Cloning, Expression, Purification and Crystallization of the PR Domain of Human Retinoblastoma Protein-Binding Zinc Finger Protein 1 (RIZ1) 2008-06-02 doi: 10.3390/ijms9060943 Wanpeng Sun C. Ronald Geyer Jian Yang http://www.mdpi.com/1422-0067/9/5/736/ BjVIII is a new myotoxic Lys49-PLA2 isolated from Bothrops jararacussu venom that exhibits atypical effects on human platelet aggregation. To better understand the mode of action of BjVIII, crystallographic studies were initiated. Two crystal forms were obtained, both containing two molecules in the asymmetric unit (ASU). Synchrotron radiation diffraction data were collected to 2.0 °A resolution and 1.9 °A resolution for crystals belonging to the space group P212121 (a = 48:4 A° , b = 65:3 A° , c = 84:3 A° ) and space group P3121 (a = b = 55:7 A° , c = 127:9 A° ), respectively. Refinement is currently in progress and the refined structures are expected to shed light on the unusual platelet aggregation activity observed for BjVIII. http://www.mdpi.com/1422-0067/9/5/736/ Thu, 08 May 2008 00:00:00 CEST International Journal of Molecular Sciences 2008-05-08 9 5 Article 736 750 1422-0067 Purification and Preliminary Crystallographic Analysis of a New Lys49-PLA2 from B. Jararacussu 2008-05-08 doi: 10.3390/ijms9050736 Marcelo L. dos Santos Fábio H. R. Fagundes Bruno R. F. Teixeira Marcos H. Toyama Ricardo Aparicio http://www.mdpi.com/1422-0067/8/10/1039/ We have isolated ribulose-1,5-bisphosphate-carboxylase/oxygenase (RUBISCO)from the red algae Galdieria Sulphuraria. The protein crystallized in two different crystalforms, the I422 crystal form being obtained from high salt and the P21 crystal form beingobtained from lower concentration of salt and PEG. We report here the crystallization,preliminary stages of structure determination and the detection of the structural phasetransition in the P21 crystal form of G. sulphuraria RUBISCO. This red algae enzymebelongs to the hexadecameric class (L8S8) with an approximate molecular weight 0.6MDa.The phase transition in G. sulphuraria RUBISCO leads from two hexadecamers to a singlehexadecamer per asymmetric unit. The preservation of diffraction power in a phasetransition for such a large macromolecule is rare. http://www.mdpi.com/1422-0067/8/10/1039/ Tue, 23 Oct 2007 00:00:00 CEST International Journal of Molecular Sciences 2007-10-23 8 10 Article 1039 1051 1422-0067 Crystallization and Characterization of Galdieria sulphuraria RUBISCO in Two Crystal Forms: Structural Phase Transition Observed in P21 Crystal Form 2007-10-23 doi: 10.3390/i8101039 Michael Baranowski Boguslaw Stec