| Int. J. Mol. Sci. (ISSN 1422-0067, CODEN: IJMCFK) |
Special
Issue: "Protein Crystallography" The special issue belongs to the section "Biochemistry, Molecular Biology and Biophysics" |
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[Editors] [Call for Papers][Announced Papers] [Published Papers] [Leading Review Papers] [List of Keywords] [Additional Instructions for authors] [Submit a manuscript]
Rationale
for
the special issue on
This Picture was prepared using the PyMOL software
Dear Colleague,
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
Lumazine synthase, catalyzes one of the final
steps in the synthesis of riboflavin in plants,
fungi, and microorganisms
Guest Editor:
Prof. Ricardo Aparicio
Structural Biology Laboratory
Institute of Chemistry - State University of Campinas (Unicamp) Campinas - SP –Brazil - CP6154 – CEP13084-862
Tel.: +(55)(19)3521-1105 Fax: +(55)(19)3521-3023
Email: aparicio@iqm.unicamp.br
Structural Biology Laboratory
Institute of Chemistry - State University of Campinas (Unicamp) Campinas - SP –Brazil - CP6154 – CEP13084-862
Tel.: +(55)(19)3521-1105 Fax: +(55)(19)3521-3023
Email: aparicio@iqm.unicamp.br
Keywords:
Topics
of special interest include, but are not strictly limited to, the
following:
- 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
The deadline for submissions is 1 May 2008
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.
Call for
Papers: download
the call for paper message here
Manuscript Submission: You are invited to submit your manuscripts online at http://submit.mdpi.org/index.php or by email to ijms@mdpi.org
Manuscript Submission: You are invited to submit your manuscripts online at http://submit.mdpi.org/index.php or by email to ijms@mdpi.org
Announced Papers:
Type: Article
Title: Microseeding – A Powerful Tool for Crystallizing Proteins in Complex with Hydrolysable Substrates
Authors: Christine Oswald , Sander H. J. Smits and Lutz Schmitt *
Affiliations: Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany;
* Author to whom correspondence should be addressed; E-mail: lutz.schmitt@uni-duesseldorf.de
Type: Article
Title: Purification and preliminary crystallographic analysis of a new Lys49-PLA2 from B. jararacussu
Authors: Marcelo L. dos Santos1, Fábio H. R. Fagundes2, Bruno R. F. Teixeira1, Marcos H. Toyama3 and Ricardo Aparicio1,*
* Author to whom correspondence should be addressed; E-mail: aparicio@iqm.unicamp.br
Published Papers:
Michael Baranowski 1 and Boguslaw Stec 2,*
1 Department of Chemistry, University of Texas at El Paso, 500 W. University Ave. El Paso, TX 79968, USA
2 Burnham Institute for Medical Research, 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA
* Author to whom correspondence should be addressed; E-mail: bstec@burnham.org
Received: 13 July 2007; in revised form: 15 October 2007 / Accepted: 16 October 2007 / Published: 23 October 2007
Full Research Paper: Crystallization and Characterization of Galdieria sulphuraria RUBISCO in Two Crystal Forms: Structural Phase Transition Observed in P21 Crystal Form
Int. J. Mol. Sci. 2007, 8, 1039-1051 (PDF format, 2340K)
Marcelo L. dos Santos 1, Fábio H. R. Fagundes 2, Bruno R. F. Teixeira 1, Marcos H. Toyama 3 and Ricardo Aparicio 1,*
1 Laboratório de Biologia Estrutural e Cristalografia, Instituto de Química, Universidade Estadual de Campinas, CP 6154, 13083-970, Campinas-SP, Brazil
2 Instituto de Biologia, Universidade Estadual de Campinas, Campinas-SP, Brazil
3 Laboratório de Química de Macromoléculas, UNESP/CLP, São Vicente-SP, Brazil
* Author to whom correspondance should be addressed; E-mail: aparicio@iqm.unicamp.br
Received: 4 February 2008; in revised form: 6 March 2008 / Accepted: 22 March 2008 / Published: 8 May 2008
Article: Purification and Preliminary Crystallographic Analysis of a New Lys49-PLA2 from B. Jararacussu
Int. J. Mol. Sci. 2008, 9, 736-750 (PDF format, 750K)
Type: Article
Title: Recent Advances in the Crank Automated Macromolecular Software Suite
Authors: Navraj S. Pannu *, Pavol Skubak, Irakli Sikharulidze, Jan Pieter Abrahams, R.A.G de Graaff
Affiliations: Department of Biophysical Structural Chemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands;
* Author to whom correspondence should be addressed. E-mail: raj@chem.leidenuniv.nl
[2] http://www.bfsc.leidenuniv.nl/software/crank/tests/pipeline1.html
[3] Skubak et al. (2005) Acta Cryst D61, 1626-1635.
Title: Recent Advances in the Crank Automated Macromolecular Software Suite
Authors: Navraj S. Pannu *, Pavol Skubak, Irakli Sikharulidze, Jan Pieter Abrahams, R.A.G de Graaff
Affiliations: Department of Biophysical Structural Chemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands;
* Author to whom correspondence should be addressed. E-mail: raj@chem.leidenuniv.nl
Abstract:
For its first release, the Crank system was shown to effectively detect
and phase anomalous scatterers from SAD data [1]. Since then, Crank's
speed and robustness has improved to build many structures
automatically for SAD, SIRAS, MAD and MAD + native data [2]. One
improvement involves using Luzzati parameters refined in the program
BP3 to validate
the quality and completeness of a substructure obtained. This has
proven to be very effective and reliable in identifying correct
solutions that do not meet the figure of merit levels reported in
substructure detection programs to safely assume a correct solution and
thus can allow for the early termination of the substructure detection
stage. To improve automated model building, an
interface to ARP/wARP and REFMAC has been added to also include SAD
data directly in model refinement. This multivariate SAD likelihood
function, implemented in a modified version of REFMAC has been shown to
extend the resolution and phase quality limits required in automated
model building with iterative refinement [3] and recently shown to be
very effective in combination with the SHELX[C/D/E] pipeline available
in CRANK. The above and other advances are available
in the latest version of Crank which is available
at http://www.bfsc.leidenuniv.nl/software/crank/ and from the CCP4
pre-release zone http://www.ccp4.ac.uk/prerelease_page.php.
[1] Ness et al. (2004) Structure, 12, 1763-1761.[2] http://www.bfsc.leidenuniv.nl/software/crank/tests/pipeline1.html
[3] Skubak et al. (2005) Acta Cryst D61, 1626-1635.
Type: Article
Title: Structural and Functional Characterization of the Norovirus RNA-dependent RNA Polymerase
Authors: Martin Högbom 1,#, Ivonne Robel 2,#, Katrin Jäger 2, Torsten Unge 1, Alwyn Jones 1 and Jacques Rohayem 2,*
Affiliations: 1 Institute of Cell & Molecular Biology, Uppsala Universitet, Uppsala, Sweden; 2 The Calicilab, Institute of Virology, Dresden UNiversity of Technology, Dresden, Germany; * Author to whom correspondence should be addressed; Jacques Rohayem, The Calicilab, Institute of Virology, Dresden University of Technology, Fiedlerstrasse 42, 01307 Dresden, Germany; Email: Jacques.Rohayem@tu-dresden.de; # Both authors contributed equally to this work.
Title: Structural and Functional Characterization of the Norovirus RNA-dependent RNA Polymerase
Authors: Martin Högbom 1,#, Ivonne Robel 2,#, Katrin Jäger 2, Torsten Unge 1, Alwyn Jones 1 and Jacques Rohayem 2,*
Affiliations: 1 Institute of Cell & Molecular Biology, Uppsala Universitet, Uppsala, Sweden; 2 The Calicilab, Institute of Virology, Dresden UNiversity of Technology, Dresden, Germany; * Author to whom correspondence should be addressed; Jacques Rohayem, The Calicilab, Institute of Virology, Dresden University of Technology, Fiedlerstrasse 42, 01307 Dresden, Germany; Email: Jacques.Rohayem@tu-dresden.de; # Both authors contributed equally to this work.
Abstract: Norovirus is a
leading cause of gastroenteritis worldwide and a major public health
concern. So far, the replication strategy of norovirus remains poorly
understood, mainly because of the lack of a cell system to cultivate
the virus. In this study, the function and the structure of a key viral
enzyme of replication, the RNA-dependent RNA polymerase (3D-like
polymerase, 3DLpol), was examined. Therefore and in a first step, the
3DLpol (YGDD) and its active site mutants (YGD343GD344G, YGD343GD, and
YGDD344G) were expressed in E. coli and purified to a milligram
concentration. Mutation of the active site completely abolished RNA
synthesis, except in the presence of Mn2+ where one mutant(YGD343GD)
exhibited a residual RNA-dependent RNA activity. In the next step, the
overall structure of the norovirus 3DLpol was determined by X-Ray
crystallography to a 2.30 Å resolution, revealing a right-hand fold
typical of the template-dependent polynucleotide polymerases.
Interestingly, the carboxyl terminus is located within the active site
cleft, as observed in the RdRp of the related human pathogenic
sapovirus. Kinetic analysis suggested that the active form of the
enzyme is a dimer, displaying a concentrationdependent cooperative
activity. Sequential deletion of the C-terminus of the protein led to
complete loss of its solubility, indicating that the C-terminus is
involved in protein-protein interactions. This experimental data on the
structure and function of the norovirus RNAdependent RNA polymerase may
set the cornerstone for the development of polymerase inhibitors to
control the infection with the norovirus, a medically relevant pathogen.
Type: Article
Title: Microseeding – A Powerful Tool for Crystallizing Proteins in Complex with Hydrolysable Substrates
Authors: Christine Oswald , Sander H. J. Smits and Lutz Schmitt *
Affiliations: Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany;
* Author to whom correspondence should be addressed; E-mail: lutz.schmitt@uni-duesseldorf.de
Abstract: Hydrolysis presents
an often-encountered obstacle in the crystallization of proteins in
complex 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, hydrolysis of unstable ligand
frequently occurs. In cases where the crystallization conditions
exhibit non-neutral pH values or require the presence of certain ions,
the phenomenon of hydrolysis might be even enhanced. During crystal
structure determination of ChoX, the substrate binding protein of a
choline specific ABC-importer from S. meliloti, we encountered the
problem of hydrolsis-sensitive protein-ligand complexes. Crystals of
ChoX in complex with choline or acetylcholine were obtained within one
month using the hanging drop methodology. However, in the case of the
ChoX/acetylcholine crystals, only choline, the hydrolysis product of
acetylcholine, was detected in the binding site. To overcome this
obstacle, we established microseeding leading to crystals of ChoX with
bound acetylcholine within 24 hours that allowed us to subsequently
determine the structure of this proteinligand complex. However, we also
encountered that all crystals obtained through this microseeding
procedure were nearly perfect pseudo merohedral twins, likely due to
the seeding-induced, rapid crystal growth.
Type: Article
Title: Purification and preliminary crystallographic analysis of a new Lys49-PLA2 from B. jararacussu
Authors: Marcelo L. dos Santos1, Fábio H. R. Fagundes2, Bruno R. F. Teixeira1, Marcos H. Toyama3 and Ricardo Aparicio1,*
* Author to whom correspondence should be addressed; E-mail: aparicio@iqm.unicamp.br
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 ASU. Synchrotron radiation diffraction
data were collected to 2.0 Å resolution and 1.9 Å resolution for
crystals belonging to the space group P212121 (a = 48.4 Å, b = 65.3 Å,
c = 84.3 Å) and space group P3121 (a = b = 55.7 Å, c = 127.9 Å),
respectively. Refinement is currently in progress and the refined
structures are expected to shed light on the unusual platelet
aggregation activity observed for BjVIII.
Type: Article
Title: Cloning, Expression, Purification and Crystallization of the PR Domain of Human Retinoblastoma Protein-binding Zinc Finger Protein 1 (RIZ1)
Authors: Wanpeng Sun 1, C. Ronald Geyer 2 and Jian Yang 1,*
Affiliations: 1 College of Pharmacy and Nutrition, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada, E-mail: w.sun@usask.ca. E-mail: jian.yang@usask.ca; 2 Department of Biochemistry, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada, E-mail: ron.geyer@usask.ca; * Author to whom correspondence should be addressed; E-mail: jian.yang@usask.ca
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 except that RIZ2 lacks an Nterminal PR domain with methyltransferase activity. Previous studies have shown that overexpression 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.
Type: Article
Title: Cloning, Expression, Purification and Crystallization of the PR Domain of Human Retinoblastoma Protein-binding Zinc Finger Protein 1 (RIZ1)
Authors: Wanpeng Sun 1, C. Ronald Geyer 2 and Jian Yang 1,*
Affiliations: 1 College of Pharmacy and Nutrition, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada, E-mail: w.sun@usask.ca. E-mail: jian.yang@usask.ca; 2 Department of Biochemistry, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada, E-mail: ron.geyer@usask.ca; * Author to whom correspondence should be addressed; E-mail: jian.yang@usask.ca
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 except that RIZ2 lacks an Nterminal PR domain with methyltransferase activity. Previous studies have shown that overexpression 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.
Published Papers:
Michael Baranowski 1 and Boguslaw Stec 2,*
1 Department of Chemistry, University of Texas at El Paso, 500 W. University Ave. El Paso, TX 79968, USA
2 Burnham Institute for Medical Research, 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA
* Author to whom correspondence should be addressed; E-mail: bstec@burnham.org
Received: 13 July 2007; in revised form: 15 October 2007 / Accepted: 16 October 2007 / Published: 23 October 2007
Full Research Paper: Crystallization and Characterization of Galdieria sulphuraria RUBISCO in Two Crystal Forms: Structural Phase Transition Observed in P21 Crystal Form
Int. J. Mol. Sci. 2007, 8, 1039-1051 (PDF format, 2340K)
Marcelo L. dos Santos 1, Fábio H. R. Fagundes 2, Bruno R. F. Teixeira 1, Marcos H. Toyama 3 and Ricardo Aparicio 1,*
1 Laboratório de Biologia Estrutural e Cristalografia, Instituto de Química, Universidade Estadual de Campinas, CP 6154, 13083-970, Campinas-SP, Brazil
2 Instituto de Biologia, Universidade Estadual de Campinas, Campinas-SP, Brazil
3 Laboratório de Química de Macromoléculas, UNESP/CLP, São Vicente-SP, Brazil
* Author to whom correspondance should be addressed; E-mail: aparicio@iqm.unicamp.br
Received: 4 February 2008; in revised form: 6 March 2008 / Accepted: 22 March 2008 / Published: 8 May 2008
Article: Purification and Preliminary Crystallographic Analysis of a New Lys49-PLA2 from B. Jararacussu
Int. J. Mol. Sci. 2008, 9, 736-750 (PDF format, 750K)
- Dauter, Z. Current state and prospects of macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 2006, 62, 1-11. Review.
- 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, 413-23. Review.
- Blundell, T. L.; Patel, S. High-throughput X-ray crystallography for drug discovery. Curr. Opin. Pharmacol. 2004, 4, 490-6. Review.
- 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, 1170-83. Review.
- 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, 2718-36. Review.
- Kleywegt, G. J.; Jones, T. A. Homo crystallographicus - quo vadis? Structure 2002, 10, 465-72.
- 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, 417-36.
- 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, 313-24. Review.
- 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.
- Lundstrom, K. Structural genomics for membrane proteins. Cell. Mol. Life Sci. 2006, 63, 2597-607. Review.
- Sali, A,; Glaeser, R.; Earnest, T.; Baumeister, W. From words to literature in structural proteomics. Nature 2003, 422, 216-25. Review.
- Chiu, W.; Baker, M. L.; Almo, S. C. Structural biology of cellular machines. Trends Cell Biol. 2006, 16, 144-50. Review.
- Liljas, A. On the complementarity of methods in structural biology. Acta Crystallogr. D Biol. Crystallogr. 2006, 62, 941-5. Review.
- 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.
- 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.