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2005
Vergara A, Lorber B, Sauter C, Giege R, Zagari A
Lessons from crystals grown in the Advanced Protein Crystallisation Facility for conventional crystallisation applied to structural biology Article de journal
Dans: Biophys Chem, vol. 118, no. 2-3, p. 102-112, 2005, ISBN: 16150532, (0301-4622 (Print) Journal Article Review).
Résumé | Liens | BibTeX | Étiquettes: FRUGIER, GIEGE Animals *Biological Sciences Crystallization Equipment Design Humans Protein Conformation Proteins/*chemistry Research Support, Non-U.S. Gov't X-Ray Diffraction, SAUTER, Unité ARN
@article{,
title = {Lessons from crystals grown in the Advanced Protein Crystallisation Facility for conventional crystallisation applied to structural biology},
author = {A Vergara and B Lorber and C Sauter and R Giege and A Zagari},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16150532},
isbn = {16150532},
year = {2005},
date = {2005-01-01},
journal = {Biophys Chem},
volume = {118},
number = {2-3},
pages = {102-112},
abstract = {The crystallographic quality of protein crystals that were grown in microgravity has been compared to that of crystals that were grown in parallel on earth gravity under otherwise identical conditions. A goal of this comparison was to assess if a more accurate 3D-structure can be derived from crystallographic analysis of the former crystals. Therefore, the properties of crystals prepared with the Advanced Protein Crystallisation Facility (APCF) on earth and in orbit during the last decade were evaluated. A statistical analysis reveals that about half of the crystals produced under microgravity had a superior X-ray diffraction limit with respect of terrestrial controls. Eleven protein structures could be determined at previously unachieved resolutions using crystals obtained in the APCF. Microgravity induced features of the most relevant structures are reported. A second goal of this study was to identify the cause of the crystal quality enhancement useful for structure determination. No correlations between the effect of microgravity and other system-dependent parameters, such as isoelectric point or crystal solvent content, were found except the reduced convection during the crystallisation process. Thus, crystal growth under diffusive regime appears to be the key parameter explaining the beneficial effect of microgravity on crystal quality. The mimicry of these effects on earth in gels or in capillary tubes is discussed and the practical consequences for structural biology highlighted.},
note = {0301-4622 (Print)
Journal Article
Review},
keywords = {FRUGIER, GIEGE Animals *Biological Sciences Crystallization Equipment Design Humans Protein Conformation Proteins/*chemistry Research Support, Non-U.S. Gov't X-Ray Diffraction, SAUTER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The crystallographic quality of protein crystals that were grown in microgravity has been compared to that of crystals that were grown in parallel on earth gravity under otherwise identical conditions. A goal of this comparison was to assess if a more accurate 3D-structure can be derived from crystallographic analysis of the former crystals. Therefore, the properties of crystals prepared with the Advanced Protein Crystallisation Facility (APCF) on earth and in orbit during the last decade were evaluated. A statistical analysis reveals that about half of the crystals produced under microgravity had a superior X-ray diffraction limit with respect of terrestrial controls. Eleven protein structures could be determined at previously unachieved resolutions using crystals obtained in the APCF. Microgravity induced features of the most relevant structures are reported. A second goal of this study was to identify the cause of the crystal quality enhancement useful for structure determination. No correlations between the effect of microgravity and other system-dependent parameters, such as isoelectric point or crystal solvent content, were found except the reduced convection during the crystallisation process. Thus, crystal growth under diffusive regime appears to be the key parameter explaining the beneficial effect of microgravity on crystal quality. The mimicry of these effects on earth in gels or in capillary tubes is discussed and the practical consequences for structural biology highlighted.
2004
Delarue M, Dumas P
On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 101, no. 18, p. 6957-6962, 2004, ISBN: 15096585, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: DUMAS Carrier Proteins/chemistry Computer Simulation Escherichia coli Proteins/chemistry *Models, Molecular Proteins/*chemistry Support, Non-U.S. Gov't X-Ray Diffraction, Unité ARN
@article{,
title = {On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models},
author = {M Delarue and P Dumas},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15096585},
doi = {10.1073/pnas.0400301101},
isbn = {15096585},
year = {2004},
date = {2004-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {101},
number = {18},
pages = {6957-6962},
abstract = {As more and more structures of macromolecular complexes get solved in different conditions, it has become apparent that flexibility is an inherent part of their biological function. Normal mode analysis using simplified models of proteins such as the elastic network model has proved very effective in showing that many of the structural transitions derived from a survey of the Protein Data Bank can be explained by just a few of the lowest-frequency normal modes. In this work, normal modes are used to carry out medium- or low-resolution structural refinement, enforcing collective and large-amplitude movements that are beyond the reach of existing methods. Refinement is carried out in reciprocal space with respect to the normal mode amplitudes, by using standard conjugate-gradient minimization. Several tests on synthetic diffraction data whose mode concentration follows the one of real movements observed in the Protein Data Bank have shown that the radius of convergence is larger than the one of rigid-body refinement. Tests with experimental diffraction data for the same protein in different environments also led to refined structural models showing drastic reduction of the rms deviation with the target model. Because the structural transition is described by very few parameters, over-fitting of real experimental data is easily detected by using a cross-validation test. The method has also been applied to the refinement of atomic models into molecular envelopes and could readily be used to fit large macromolecular complex rearrangements into cryo-electron microscopy-reconstructed images as well as small-angle x-ray scattering-derived envelopes.},
note = {0027-8424
Journal Article},
keywords = {DUMAS Carrier Proteins/chemistry Computer Simulation Escherichia coli Proteins/chemistry *Models, Molecular Proteins/*chemistry Support, Non-U.S. Gov't X-Ray Diffraction, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
As more and more structures of macromolecular complexes get solved in different conditions, it has become apparent that flexibility is an inherent part of their biological function. Normal mode analysis using simplified models of proteins such as the elastic network model has proved very effective in showing that many of the structural transitions derived from a survey of the Protein Data Bank can be explained by just a few of the lowest-frequency normal modes. In this work, normal modes are used to carry out medium- or low-resolution structural refinement, enforcing collective and large-amplitude movements that are beyond the reach of existing methods. Refinement is carried out in reciprocal space with respect to the normal mode amplitudes, by using standard conjugate-gradient minimization. Several tests on synthetic diffraction data whose mode concentration follows the one of real movements observed in the Protein Data Bank have shown that the radius of convergence is larger than the one of rigid-body refinement. Tests with experimental diffraction data for the same protein in different environments also led to refined structural models showing drastic reduction of the rms deviation with the target model. Because the structural transition is described by very few parameters, over-fitting of real experimental data is easily detected by using a cross-validation test. The method has also been applied to the refinement of atomic models into molecular envelopes and could readily be used to fit large macromolecular complex rearrangements into cryo-electron microscopy-reconstructed images as well as small-angle x-ray scattering-derived envelopes.
Auffinger P, Bielecki L, Westhof E
Anion binding to nucleic acids Article de journal
Dans: Structure, vol. 12, no. 3, p. 379-388, 2004, ISBN: 15016354, (0969-2126 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anions/chemistry/*metabolism Computer Simulation Databases, Molecular Nucleic Acids/chemistry/*metabolism Support, Non-U.S. Gov't X-Ray Diffraction, Nucleic Acid Models, Unité ARN, WESTHOF
@article{,
title = {Anion binding to nucleic acids},
author = {P Auffinger and L Bielecki and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15016354},
isbn = {15016354},
year = {2004},
date = {2004-01-01},
journal = {Structure},
volume = {12},
number = {3},
pages = {379-388},
abstract = {Nucleic acids are generally considered as efficient cation binders. Therefore, the likelihood that negatively charged ions might intrude their first hydration shell is rarely considered. Here, we show on the basis of (i) a survey of the Nucleic Acid Database, (ii) several structures extracted from the Cambridge Structural Database, and (iii) molecular dynamics simulations, that the nucleotide electropositive edges involving mainly amino, imino, and hydroxyl groups can cast specific anion binding sites. These binding sites constitute also good locations for the binding of the negatively charged groups of the Asp and Glu residues or the nucleic acid phosphate groups. Furthermore, it is observed in several instances that anions, like water molecules and cations, do mediate protein/nucleic acid interactions. Thus, anions as well as negatively charged groups are directly involved in specific recognition and folding phenomena involving polyanionic nucleic acids.},
note = {0969-2126
Journal Article},
keywords = {Anions/chemistry/*metabolism Computer Simulation Databases, Molecular Nucleic Acids/chemistry/*metabolism Support, Non-U.S. Gov't X-Ray Diffraction, Nucleic Acid Models, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Nucleic acids are generally considered as efficient cation binders. Therefore, the likelihood that negatively charged ions might intrude their first hydration shell is rarely considered. Here, we show on the basis of (i) a survey of the Nucleic Acid Database, (ii) several structures extracted from the Cambridge Structural Database, and (iii) molecular dynamics simulations, that the nucleotide electropositive edges involving mainly amino, imino, and hydroxyl groups can cast specific anion binding sites. These binding sites constitute also good locations for the binding of the negatively charged groups of the Asp and Glu residues or the nucleic acid phosphate groups. Furthermore, it is observed in several instances that anions, like water molecules and cations, do mediate protein/nucleic acid interactions. Thus, anions as well as negatively charged groups are directly involved in specific recognition and folding phenomena involving polyanionic nucleic acids.