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Protein Crystallography
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Protein Crystallography

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (30 September 2008) | Viewed by 41887

Special Issue Editor

Prof. Dr. Ricardo Aparicio

E-Mail Website
Guest Editor
Laboratory of Structural Biology and Crystallography Institute of Chemistry, University of Campinas (UNICAMP) Campinas, SP, Brazil
Interests: structural biology; protein crystallography; SAXS

Special Issue Information

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

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)

Keywords

  • X-ray diffraction Protein Crystallography
  • structural biology
  • structural genomics
  • cloning
  • expression
  • purification and crystallization
  • preliminary crystallographic analysis
  • protein structure analysis
  • structure-function relationships
  • advances in protein crystallization and methodology
  • high-throughput methods
  • structure-based drug design
  • enzymatic reaction mechanisms
  • protein molecular mechanisms
  • protein-protein interactions
  • membrane proteins
  • small-angle X-ray scattering of biological macromolecules
  • macromolecular complexes
  • protein structural databases
  • time-resolved Macromolecular Crystallography

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Published Papers (4 papers)

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1312 KiB  
Article
Microseeding – A Powerful Tool for Crystallizing Proteins Complexed with Hydrolyzable Substrates
by Christine Oswald, Sander H. J. Smits, Erhard Bremer and Lutz Schmitt
Int. J. Mol. Sci. 2008, 9(7), 1131-1141; https://doi.org/10.3390/ijms9071131 - 8 Jul 2008
Cited by 8 | Viewed by 11880
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Protein Crystallography)
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367 KiB  
Article
Cloning, Expression, Purification and Crystallization of the PR Domain of Human Retinoblastoma Protein-Binding Zinc Finger Protein 1 (RIZ1)
by Wanpeng Sun, C. Ronald Geyer and Jian Yang
Int. J. Mol. Sci. 2008, 9(6), 943-950; https://doi.org/10.3390/ijms9060943 - 2 Jun 2008
Cited by 8 | Viewed by 9926
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Protein Crystallography)
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750 KiB  
Article
Purification and Preliminary Crystallographic Analysis of a New Lys49-PLA2 from B. Jararacussu
by Marcelo L. Dos Santos, Fábio H. R. Fagundes, Bruno R. F. Teixeira, Marcos H. Toyama and Ricardo Aparicio
Int. J. Mol. Sci. 2008, 9(5), 736-750; https://doi.org/10.3390/ijms9050736 - 8 May 2008
Cited by 8 | Viewed by 10012
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Protein Crystallography)
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2578 KiB  
Article
Crystallization and Characterization of Galdieria sulphuraria RUBISCO in Two Crystal Forms: Structural Phase Transition Observed in P21 Crystal Form
by Michael Baranowski and Boguslaw Stec
Int. J. Mol. Sci. 2007, 8(10), 1039-1051; https://doi.org/10.3390/i8101039 - 23 Oct 2007
Cited by 4 | Viewed by 9374
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Protein Crystallography)
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