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  • 1
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    Influence of interior packing and hydrophobicity on the stability of a protein (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-07-07
    Description: Protein interiors contain many tightly packed apolar atoms in a nearly crystalline state. Both shielding of apolar atoms from solvent and efficient interior packing arrangements affect protein stability, but their relative importance is unclear. To separate these effects, the stabilities of wild-type and mutant gene V proteins from bacteriophage fl were studied by measuring resistance to denaturation. The effects of subtle interior packing changes, both separate from and combined with changes in buried side chain hydrophobicity, were measured. For the interior apolar-to-apolar substitutions studied, the two effects were of the same magnitude and alteration of packing without accompanying hydrophobicity changes substantially destabilized the protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sandberg, W S -- Terwilliger, T C -- 5732 GM07281/GM/NIGMS NIH HHS/ -- GM38714/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1989 Jul 7;245(4913):54-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2787053" target="_blank"〉PubMed〈/a〉
    Keywords: Calorimetry ; Coliphages/genetics ; Drug Stability ; Guanidine ; Guanidines ; Models, Molecular ; Mutation ; *Protein Conformation ; Protein Denaturation ; *Viral Proteins/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Improved molecular replacement by density- and energy-guided protein structure optimization (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-05-03
    Description: Molecular replacement procedures, which search for placements of a starting model within the crystallographic unit cell that best account for the measured diffraction amplitudes, followed by automatic chain tracing methods, have allowed the rapid solution of large numbers of protein crystal structures. Despite extensive work, molecular replacement or the subsequent rebuilding usually fail with more divergent starting models based on remote homologues with less than 30% sequence identity. Here we show that this limitation can be substantially reduced by combining algorithms for protein structure modelling with those developed for crystallographic structure determination. An approach integrating Rosetta structure modelling with Autobuild chain tracing yielded high-resolution structures for 8 of 13 X-ray diffraction data sets that could not be solved in the laboratories of expert crystallographers and that remained unsolved after application of an extensive array of alternative approaches. We estimate that the new method should allow rapid structure determination without experimental phase information for over half the cases where current methods fail, given diffraction data sets of better than 3.2 A resolution, four or fewer copies in the asymmetric unit, and the availability of structures of homologous proteins with 〉20% sequence identity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365536/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365536/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DiMaio, Frank -- Terwilliger, Thomas C -- Read, Randy J -- Wlodawer, Alexander -- Oberdorfer, Gustav -- Wagner, Ulrike -- Valkov, Eugene -- Alon, Assaf -- Fass, Deborah -- Axelrod, Herbert L -- Das, Debanu -- Vorobiev, Sergey M -- Iwai, Hideo -- Pokkuluri, P Raj -- Baker, David -- 082961/Wellcome Trust/United Kingdom -- 5R01GM092802/GM/NIGMS NIH HHS/ -- GM074898/GM/NIGMS NIH HHS/ -- P01 GM063210/GM/NIGMS NIH HHS/ -- P41RR002250/RR/NCRR NIH HHS/ -- R01 GM092802/GM/NIGMS NIH HHS/ -- U54 GM074898/GM/NIGMS NIH HHS/ -- U54 GM074958/GM/NIGMS NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- U54GM074958/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- Wellcome Trust/United Kingdom -- England -- Nature. 2011 May 26;473(7348):540-3. doi: 10.1038/nature09964. Epub 2011 May 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Washington, Department of Biochemistry and HHMI, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21532589" target="_blank"〉PubMed〈/a〉
    Keywords: Computational Biology/*methods ; Crystallography, X-Ray ; Databases, Protein ; Electrons ; *Models, Molecular ; Proteins/*chemistry ; Sequence Alignment ; Sequence Homology, Amino Acid ; *Structural Homology, Protein
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-08-12
    Description: Clustered regularly interspaced short palindromic repeats (CRISPRs) are essential components of RNA-guided adaptive immune systems that protect bacteria and archaea from viruses and plasmids. In Escherichia coli, short CRISPR-derived RNAs (crRNAs) assemble into a 405-kilodalton multisubunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Here we present the 3.24 angstrom resolution x-ray crystal structure of Cascade. Eleven proteins and a 61-nucleotide crRNA assemble into a seahorse-shaped architecture that binds double-stranded DNA targets complementary to the crRNA-guide sequence. Conserved sequences on the 3' and 5' ends of the crRNA are anchored by proteins at opposite ends of the complex, whereas the guide sequence is displayed along a helical assembly of six interwoven subunits that present five-nucleotide segments of the crRNA in pseudo-A-form configuration. The structure of Cascade suggests a mechanism for assembly and provides insights into the mechanisms of target recognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4188430/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4188430/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jackson, Ryan N -- Golden, Sarah M -- van Erp, Paul B G -- Carter, Joshua -- Westra, Edze R -- Brouns, Stan J J -- van der Oost, John -- Terwilliger, Thomas C -- Read, Randy J -- Wiedenheft, Blake -- 082961/Wellcome Trust/United Kingdom -- 082961/Z/07/Z/Wellcome Trust/United Kingdom -- 100140/Wellcome Trust/United Kingdom -- 52006931/Howard Hughes Medical Institute/ -- F32 GM108436/GM/NIGMS NIH HHS/ -- GM063210/GM/NIGMS NIH HHS/ -- P01 GM063210/GM/NIGMS NIH HHS/ -- P20GM103500/GM/NIGMS NIH HHS/ -- P41GM103393/GM/NIGMS NIH HHS/ -- R01 GM108888/GM/NIGMS NIH HHS/ -- R01GM108888/GM/NIGMS NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Sep 19;345(6203):1473-9. doi: 10.1126/science.1256328. Epub 2014 Aug 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA. ; Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, Netherlands. ; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. ; Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, UK. ; Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA. bwiedenheft@gmail.com.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25103409" target="_blank"〉PubMed〈/a〉
    Keywords: CRISPR-Associated Proteins/*chemistry ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Crystallography, X-Ray ; Escherichia coli/*genetics ; Escherichia coli Proteins/*chemistry ; RNA Editing ; RNA, Bacterial/*chemistry ; RNA, Guide/*chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
    Electronic Resource
    Electronic Resource
    Isomorphous replacement: effects of errors on the phase probability distribution. Erratum (1987)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 43 (1987), S. 286-286 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In the paper by Terwilliger & Eisenberg [Acta Cryst. (1987). A43, 6-13], equation (18) should read {\bar F}_{PH} \equiv {{1}\over{2}} (|{\rm {\bf F}^{+}_{{\bf PH}}}| + |{\rm {\bf F}^{-}_{{\bf PH}}}| = |{\rm {\bf F}_{{\bf PH}}}|. \eqno (18)
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767387099409
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  • 5
    Electronic Resource
    Electronic Resource
    Isomorphous replacement: effects of errors on the phase probability distribution (1987)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 43 (1987), S. 6-13 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A simple framework for the analysis of the effects of errors in the method of isomorphous replacement is developed. This framework is used to derive phase probability distributions similar to those given by Blow & Crick [Acta Cryst. (1959). 12, 794-802]. The present analysis suggests an improved means of calculating the mean-square 'lack-of-closure' residuals and shows that they differ by a factor of two for centric and acentric reflections. It is also shown that the lack-of-closure residuals have a straightforward interpretation and that they may be used to estimate the error in the heavy-atom model and the degree of isomorphism between native and derivative structures if anomalous differences have been measured.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767387099987
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  • 6
    Electronic Resource
    Electronic Resource
    Bayesian Weighting for Macromolecular Crystallographic Refinement (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 743-748 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A simple weighting scheme for atomic refinement is discussed. The approach, called `Bayesian weighting', is designed to be robust with respect to the bias that arises from the incomplete nature of the atomic model, which in macromolecular crystallography is typically quite serious. Bayesian weights are based on the mean-squared residual errors over shells of resolution, with centric and acentric reflections considered separately and with allowances made for experimental uncertainties. Use of Bayesian weighting is shown in test cases typical for macromolecular crystallography to improve the accuracy of the refined coordinates when compared with schemes employing unit weights or experimental variances.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444996001473
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  • 7
    Electronic Resource
    Electronic Resource
    MAD phasing: treatment of dispersive differences as isomorphous replacement information (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 17-23 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A framework analogous to that used for the analysis of data in the method of isomorphous replacement is applied to the analysis of multi-wavelength anomalous-diffraction (MAD) data. The present method is advantageous in that refinement of parameters describing the anomalously scattering atoms in the structure can be carried out using nearly all the data, and in that phase information can be readily combined. The procedure described here involves an approximation in which it is assumed that the magnitude of the structure factor corresponding to anomalously scattering atoms in the unit cell is small compared to that corresponding to all other atoms in the structure. A model calculation is applied to a protein crystal with 682 non-H atoms in the asymmetric unit and two Se atoms as the anomalous scatterers. It is shown using this model calculation that the approximation used in this analysis does not substantially affect the accuracy of phase calculations for this MAD data. The method is demonstrated by application to MAD data collected on gene V protein.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993008236
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  • 8
    Electronic Resource
    Electronic Resource
    Bayesian Difference Refinement (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 1004-1011 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Interest in a pair of highly isomorphous structures often focuses on the differences between them. In cases where substantial correlated model errors exist or where there are differences in the quality of the two experimental data sets (cases quite common in macromolecular crystallography), independent refinement of the two structures does not lead to the most accurate estimate of the differences between them. An alternative procedure that has proven effective in some such cases is difference refinement, in which the residual between observed and calculated differences in structure-factor amplitudes between the two structures is minimized. A Bayesian approach has been used to extend the range of applicability of difference refinement to cases where there is only partial correlation in model errors and where the overlap between the data sets is limited. The resulting method, Bayesian difference refinement, uses residuals to be minimized that vary smoothly between difference refinement and independent refinement. When the errors in the two structural models are very similar, difference refinement is used; when they are very different, independent refinement is used; and when they are partially correlated, a combination of the two is used. The procedure is very simple to apply and does not significantly increase the computational demands of refinement.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444996006725
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  • 9
    Electronic Resource
    Electronic Resource
    Bayesian Correlated MAD Phasing (1997)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 53 (1997), S. 571-579 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A Bayesian treatment for phase calculation in the multiwavelength anomalous diffraction (MAD) technique is presented. This approach explicitly treats effects of errors correlated among measurements at different wavelengths and between Bijvoet pairs. The resulting method, which is called Bayesian correlated MAD phasing, gives proper statistical consideration to all data and does not give special treatment to data from a particular wavelength. Results obtained using Bayesian correlated MAD phasing and two other strategies on both a model test case and on data obtained in two actual MAD experiments are compared. Although all procedures performed well when the completeness of the data was high, it is shown that Bayesian correlated MAD phasing is more robust with respect to incompleteness of data than the other methods are. At 60% completeness the improvement over other methods for the examples given was nearly 50% in the correlation coefficients, and made a substantial difference in the interpretability of an electron-density map.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444997005398
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  • 10
    Electronic Resource
    Electronic Resource
    Correlated Phasing of Multiple Isomorphous Replacement Data (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 749-757 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Substantial highly correlated differences sometimes exist between a series of heavy-atom derivatives of a macromolecule and the native structure. Use of such a series of derivatives for phase determination by multiple isomorphous replacement (MIR) has been difficult because MIR analysis has treated errors as independent. A simple Bayesian approach has been used to derive probability distributions for the phase in the case where a group of MIR derivatives have correlated errors. The utility of the resulting `correlated-phasing' method has been examined by applying it to both simulated and real MIR data sets that contain sizeable correlated errors and it has been found that it can dramatically improve MIR phase estimates in these cases. Correlated phasing is applicable to situations where derivatives exhibit substantial correlated changes in protein conformation or crystal packing or where correlated errors in heavy-atom models are large. Correlated phasing does not substantially increase the complexity of phase computation and is suitable for routine use.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444996000832
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