Special Issue: Protein CrystallographyThis 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 “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,
Figure: Lumazine synthase, catalyzes one of the
final steps in the synthesis of riboflavin in plants,
fungi, and microorganisms. (This picture was
prepared using the PyMOL software).
Guest Editor
Prof. Dr. Ricardo Aparicio
Structural Biology Laboratory, Institute of Chemistry
State University of Campinas (Unicamp),
Campinas, CP6154 – CEP13084-862 SP, Brazil
Tel.: +55-19-3521-1105; Fax: +55-19-3521-3023
E-mail: [email protected]
Structural Biology Laboratory, Institute of Chemistry
State University of Campinas (Unicamp),
Campinas, CP6154 – CEP13084-862 SP, Brazil
Tel.: +55-19-3521-1105; Fax: +55-19-3521-3023
E-mail: [email protected]
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
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 by email to [email protected]. Add "Manuscript Submission for Protein Crystallography" as the subject of the message. Submitted papers should not have been previously published nor be currently under consideration for publication elsewhere. All papers are refereed through a peer-review process. A guide for authors, sample copies and other relevant information for submitting papers are available on the “Instructions for Authors” page. The International Journal of Molecular Sciences is a peer-reviewed, monthly journal, published by Molecular Diversity Preservation International.
You are invited to submit your manuscripts by email to [email protected]. Add "Manuscript Submission for Protein Crystallography" as the subject of the message. Submitted papers should not have been previously published nor be currently under consideration for publication elsewhere. All papers are refereed through a peer-review process. A guide for authors, sample copies and other relevant information for submitting papers are available on the “Instructions for Authors” page. The International Journal of Molecular Sciences is a peer-reviewed, monthly journal, published by Molecular Diversity Preservation International.
Announced Papers
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: [email protected]
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: [email protected]
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)
Wanpeng Sun 1, C. Ronald Geyer 2 and Jian Yang 1,*
1 College of Pharmacy and Nutrition, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada; E-maila: [email protected]; [email protected]
2 Department of Biochemistry, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada; E-mail: [email protected]
* Author to whom correspondence should be addressed; E-mail: [email protected]
Received: 2 April 2008; in revised form: 28 May 2008 / Accepted: 2 June 2008 / Published: 2 June 2008
Article: Cloning, Expression, Purification and Crystallization of the PR Domain of Human Retinoblastoma Protein-Binding Zinc Finger Protein 1 (RIZ1)
Int. J. Mol. Sci. 2008, 9, 943-950 (PDF format, 368K); DOI: 10.3390/ijms9060950
Christine Oswald 1, Sander H. J. Smits 1, Erhard Bremer 2 and Lutz Schmitt 1,*
1 Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
2 Laboratory for Microbiology, Department of Biology, Philipps University Marbrug, Karl-von-Frisch Str., 35032 Marburg, Germany
* Author to whom correspondence should be addressed: Tel. +49-211-81-10773; Fax: +49-211-81-15310; E-mail: [email protected].
Received: 3 May 2008; in revised form: 5 June 2008 / Accepted: 10 June 2008 / Published: 8 July 2008
Article: Microseeding – A Powerful Tool for Crystallizing Proteins Complexed with Hydrolyzable Substrates
Int. J. Mol. Sci. 2008, 9, 1131-1141 (PDF format, 1313K); DOI: 10.3390/ijms9071131
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: [email protected]
[2] http://www.bfsc.leidenuniv.nl/software/crank/tests/pipeline1.html
[3] Skubak et al. Acta Cryst D 2005, 61, 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: [email protected]
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. Structure 2004, 12, 1763-1761.[2] http://www.bfsc.leidenuniv.nl/software/crank/tests/pipeline1.html
[3] Skubak et al. Acta Cryst D 2005, 61, 1626-1635.
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: [email protected]
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: [email protected]
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)
Wanpeng Sun 1, C. Ronald Geyer 2 and Jian Yang 1,*
1 College of Pharmacy and Nutrition, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada; E-maila: [email protected]; [email protected]
2 Department of Biochemistry, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada; E-mail: [email protected]
* Author to whom correspondence should be addressed; E-mail: [email protected]
Received: 2 April 2008; in revised form: 28 May 2008 / Accepted: 2 June 2008 / Published: 2 June 2008
Article: Cloning, Expression, Purification and Crystallization of the PR Domain of Human Retinoblastoma Protein-Binding Zinc Finger Protein 1 (RIZ1)
Int. J. Mol. Sci. 2008, 9, 943-950 (PDF format, 368K); DOI: 10.3390/ijms9060950
Christine Oswald 1, Sander H. J. Smits 1, Erhard Bremer 2 and Lutz Schmitt 1,*
1 Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
2 Laboratory for Microbiology, Department of Biology, Philipps University Marbrug, Karl-von-Frisch Str., 35032 Marburg, Germany
* Author to whom correspondence should be addressed: Tel. +49-211-81-10773; Fax: +49-211-81-15310; E-mail: [email protected].
Received: 3 May 2008; in revised form: 5 June 2008 / Accepted: 10 June 2008 / Published: 8 July 2008
Article: Microseeding – A Powerful Tool for Crystallizing Proteins Complexed with Hydrolyzable Substrates
Int. J. Mol. Sci. 2008, 9, 1131-1141 (PDF format, 1313K); DOI: 10.3390/ijms9071131
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