251
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Rai N, Nöllmann M, Spotorno B, Tassara G, Byron O, Rocco M. SOMO (SOlution MOdeler) differences between X-Ray- and NMR-derived bead models suggest a role for side chain flexibility in protein hydrodynamics. Structure 2005; 13:723-34. [PMID: 15893663 DOI: 10.1016/j.str.2005.02.012] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Revised: 02/02/2005] [Accepted: 02/03/2005] [Indexed: 11/27/2022]
Abstract
Reduced numbers of frictional/scattering centers are essential for tractable hydrodynamic and small-angle scattering data modeling. We present a method for generating medium-resolution models from the atomic coordinates of proteins, basically by using two nonoverlapping spheres of differing radii per residue. The computed rigid-body hydrodynamic parameters of BPTI, RNase A, and lysozyme models were compared with a large database of critically assessed experimental values. Overall, very good results were obtained, but significant discrepancies between X-ray- and NMR-derived models were found. Interestingly, they could be accounted for by properly considering the extent to which highly mobile surface side chains differently affect translational/rotational properties. Models of larger structures, such as fibrinogen fragment D and citrate synthase, also produced consistent results. Foremost among this method's potential applications is the overall conformation and dynamics of modular/multidomain proteins and of supramolecular complexes. The possibility of merging data from high- and low-resolution structures greatly expands its scope.
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Affiliation(s)
- Nithin Rai
- Division of Infection & Immunity, Institute of Biomedical & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
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252
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Unser M, Sorzano C, Thévenaz P, Jonić S, El-Bez C, De Carlo S, Conway J, Trus B. Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions. J Struct Biol 2005; 149:243-55. [PMID: 15721578 PMCID: PMC1464087 DOI: 10.1016/j.jsb.2004.10.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Revised: 09/22/2004] [Indexed: 11/20/2022]
Abstract
Measuring the quality of three-dimensional (3D) reconstructed biological macromolecules by transmission electron microscopy is still an open problem. In this article, we extend the applicability of the spectral signal-to-noise ratio (SSNR) to the evaluation of 3D volumes reconstructed with any reconstruction algorithm. The basis of the method is to measure the consistency between the data and a corresponding set of reprojections computed for the reconstructed 3D map. The idiosyncrasies of the reconstruction algorithm are taken explicitly into account by performing a noise-only reconstruction. This results in the definition of a 3D SSNR which provides an objective indicator of the quality of the 3D reconstruction. Furthermore, the information to build the SSNR can be used to produce a volumetric SSNR (VSSNR). Our method overcomes the need to divide the data set in two. It also provides a direct measure of the performance of the reconstruction algorithm itself; this latter information is typically not available with the standard resolution methods which are primarily focused on reproducibility alone.
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Affiliation(s)
- M. Unser
- Biomedical Imaging Group, Swiss Federal Institute of Technology Lausanne, CH-1015 Lausanne VD, Switzerland
| | - C.O.S. Sorzano
- Biomedical Imaging Group, Swiss Federal Institute of Technology Lausanne, CH-1015 Lausanne VD, Switzerland
- Escuela Politécnica Superior, Universidad San Pablo-CEU, Campus Urb. Montepríncipe s/n, 28668 Boadilla del Monte, Madrid, Spain
- Biocomputing Unit, National Center of Biotechnology (CSIC), Campus Univ. Autónoma s/n, 28047 Cantoblanco, Madrid, Spain
- Corresponding author. Fax: +34 91 585 4506. E-mail address: (C.O.S. Sorzano)
| | - P Thévenaz
- Biomedical Imaging Group, Swiss Federal Institute of Technology Lausanne, CH-1015 Lausanne VD, Switzerland
| | - S. Jonić
- Biomedical Imaging Group, Swiss Federal Institute of Technology Lausanne, CH-1015 Lausanne VD, Switzerland
| | - C. El-Bez
- Laboratoire d’analyse ultrastructurale, Université de Lausanne, CH-1015 Lausanne VD, Switzerland
| | - S. De Carlo
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - J.F. Conway
- Laboratoire de Microscopie Electronique Structurale, Institut de Biologie Structurale, 41 rue Jules Horowitz, 38027 Grenoble, Cedex 1, France
| | - B.L. Trus
- Imaging Sciences Laboratory, Center of Information Technology (NIH/DHHS), 12 Center Drive, MSC 5624, Bethesda, MD 20892-5624, USA
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253
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254
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Affiliation(s)
- John Meurig Thomas
- Department of Materials Science, University of Cambridge, Cambridge CB2 3QZ, UK.
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255
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Fernandez J, Li S. Anisotropic Nonlinear Filtering of Cellular Structures in Cryoelectron Tomography. Comput Sci Eng 2005. [DOI: 10.1109/mcse.2005.89] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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256
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Alber F, Kim MF, Sali A. Structural characterization of assemblies from overall shape and subcomplex compositions. Structure 2005; 13:435-45. [PMID: 15766545 DOI: 10.1016/j.str.2005.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2004] [Revised: 01/12/2005] [Accepted: 01/14/2005] [Indexed: 11/24/2022]
Abstract
We suggest structure characterization of macromolecular assemblies by combining assembly shape determined by electron cyromicroscopy with information about subunit proximity determined by affinity purification. To achieve this aim, structure characterization is expressed as a problem in satisfaction of spatial restraints that (1) represents subunits as spheres, (2) encodes information about the subunit excluded volume, assembly shape, and pulldowns in a scoring function, and (3) finds subunit configurations that satisfy the input restraints by an optimization of the scoring function. Testing of the approach with model systems suggests its feasibility.
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Affiliation(s)
- Frank Alber
- Department of Biopharmaceutical Sciences and, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California 94143, USA
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257
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Bajaj C, Castrillon-Candas J, Siddavanahalli V, Xu Z. Compressed representations of macromolecular structures and properties. Structure 2005; 13:463-71. [PMID: 15766547 DOI: 10.1016/j.str.2005.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2004] [Revised: 02/10/2005] [Accepted: 02/11/2005] [Indexed: 11/21/2022]
Abstract
We introduce a new and unified, compressed volumetric representation for macromolecular structures at varying feature resolutions, as well as for many computed associated properties. Important caveats of this compressed representation are fast random data access and decompression operations. Many computational tasks for manipulating large structures, including those requiring interactivity such as real-time visualization, are greatly enhanced by utilizing this compact representation. The compression scheme is obtained by using a custom designed hierarchical wavelet basis construction. Due to the continuity offered by these wavelets, we retain very good accuracy of molecular surfaces, at very high compression ratios, for macromolecular structures at multiple resolutions.
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Affiliation(s)
- Chandrajit Bajaj
- Computational Visualization Center, Department of Computer Sciences and, Institute for Computational and Engineering Sciences, ACES 2.128, 24th & Speedway, University of Texas, Austin, Texas 78712, USA.
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258
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De S, Krishnadev O, Srinivasan N, Rekha N. Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different. BMC STRUCTURAL BIOLOGY 2005; 5:15. [PMID: 16105176 PMCID: PMC1201154 DOI: 10.1186/1472-6807-5-15] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Accepted: 08/16/2005] [Indexed: 11/26/2022]
Abstract
Background A polypeptide chain of a protein-protein complex is said to be obligatory if it is bound to another chain throughout its functional lifetime. Such a chain might not adopt the native fold in the unbound form. A non-obligatory polypeptide chain associates with another chain and dissociates upon molecular stimulus. Although conformational changes at the interaction interface are expected, the overall 3-D structure of the non-obligatory chain is unaltered. The present study focuses on protein-protein complexes to understand further the differences between obligatory and non-obligatory interfaces. Results A non-obligatory chain in a complex of known 3-D structure is recognized by its stable existence with same fold in the bound and unbound forms. On the contrary, an obligatory chain is detected by its existence only in the bound form with no evidence for the native-like fold of the chain in the unbound form. Various interfacial properties of a large number of complexes of known 3-D structures thus classified are comparatively analyzed with an aim to identify structural descriptors that distinguish these two types of interfaces. We report that the interaction patterns across the interfaces of obligatory and non-obligatory components are different and contacts made by obligatory chains are predominantly non-polar. The obligatory chains have a higher number of contacts per interface (20 ± 14 contacts per interface) than non-obligatory chains (13 ± 6 contacts per interface). The involvement of main chain atoms is higher in the case of obligatory chains (16.9 %) compared to non-obligatory chains (11.2 %). The β-sheet formation across the subunits is observed only among obligatory protein chains in the dataset. Apart from these, other features like residue preferences and interface area produce marginal differences and they may be considered collectively while distinguishing the two types of interfaces. Conclusion These results can be useful in distinguishing the two types of interfaces observed in structures determined in large-scale in the structural genomics initiatives, especially for those multi-component protein assemblies for which the biochemical characterization is incomplete.
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Affiliation(s)
- Subhajyoti De
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, 721 302, India
| | - O Krishnadev
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - N Srinivasan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - N Rekha
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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259
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Abstract
We address the question of whether or not the positions of protein-binding sites on homologous protein structures are conserved irrespective of the identities of their binding partners. First, for each domain family in the Structural Classification of Proteins (SCOP), protein-binding sites are extracted from our comprehensive database of structurally defined binary domain interactions (PIBASE). Second, the binding sites within each family are superposed using a structural alignment of its members. Finally, the degree of localization of binding sites within each family is quantified by comparing it with localization expected by chance. We found that 72% of the 1847 SCOP domain families in PIBASE have binding sites with localization values greater than expected by chance. Moreover, 554 (30%) of these families have localizations that are statistically significant (i.e., more than four standard deviations away from the mean expected by chance). In contrast, only 144 (8%) families have significantly low localization. The absence of a significant correlation of the binding site localization with the average sequence and structural conservations in a family suggests that localization can be helpful for describing the functional diversity of protein-protein interactions, complementing measures of sequence and structural conservation. Consideration of the binding site localization may also result in spatial restraints for the modeling of protein assembly structures.
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Affiliation(s)
- Dmitry Korkin
- Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, CA 94143-2552, USA
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260
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Boeckmann B, Blatter MC, Famiglietti L, Hinz U, Lane L, Roechert B, Bairoch A. Protein variety and functional diversity: Swiss-Prot annotation in its biological context. C R Biol 2005; 328:882-99. [PMID: 16286078 DOI: 10.1016/j.crvi.2005.06.001] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Revised: 06/01/2005] [Accepted: 06/05/2005] [Indexed: 11/25/2022]
Abstract
We all know that the dogma 'one gene, one protein' is obsolete. A functional protein and, likewise, a protein's ultimate function depend not only on the underlying genetic information but also on the ongoing conditions of the cellular system. Frequently the transcript, like the polypeptide, is processed in multiple ways, but only one or a few out of a multitude of possible variants are produced at a time. An overview on processes that can lead to sequence variety and structural diversity in eukaryotes is given. The UniProtKB/Swiss-Prot protein knowledgebase provides a wealth of information regarding protein variety, function and associated disorders. Examples for such annotation are shown and further ones are available at http://www.expasy.org/sprot/tutorial/examples_CRB.
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Affiliation(s)
- Brigitte Boeckmann
- Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1, rue Michel-Servet, 1211 Genève 4, Switzerland.
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261
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Dzivenu OK, Park HH, Wu H. General co-expression vectors for the overexpression of heterodimeric protein complexes in Escherichia coli. Protein Expr Purif 2005; 38:1-8. [PMID: 15477075 DOI: 10.1016/j.pep.2004.07.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Revised: 07/26/2004] [Indexed: 11/21/2022]
Abstract
We have designed and constructed a novel pair of bacterial co-expression vectors to facilitate the production of substantial amounts of recombinant multiprotein complexes for biochemical, biophysical, and structural studies. pOKD4 (kanamycin-resistant) and pOKD5 (ampicillin-resistant) are derivatives of pACYC177 cloning and pET26b expression vectors. As a result, pOKD4 and pOKD5 are T7-based expression plasmids containing the p15A origin of replication. This feature permits either pOKD4 or pOKD5 to co-exist in the same bacterial cell with most Escherichia coli expression vectors including the popular pET expression vectors. The pOKD4 and pOKD5 vectors have been engineered to possess exactly the same multiple cloning sites as pET26b thus allowing for the relatively easy shuttling of genes to and fro. The efficacy and versatility of this novel pair of co-expression vectors was successfully applied to the production of significant amounts of active DFF40/DFF45 heterodimeric protein complex in E. coli for detailed biochemical and structural studies.
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Affiliation(s)
- Oki K Dzivenu
- Department of Biochemistry, Weill Medical College, Cornell University, 1300 York Avenue, New York, NY 10021, USA.
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262
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Marsh BJ. Lessons from tomographic studies of the mammalian Golgi. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1744:273-92. [PMID: 15896857 DOI: 10.1016/j.bbamcr.2005.04.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Revised: 04/11/2005] [Accepted: 04/11/2005] [Indexed: 11/22/2022]
Abstract
Basic structure studies of the biosynthetic machinery of the cell by electron microscopy (EM) have underpinned much of our fundamental knowledge in the areas of molecular cell biology and membrane traffic. Driven by our collective desire to understand how changes in the complex and dynamic structure of this enigmatic organelle relate to its pivotal roles in the cell, the comparatively high-resolution glimpses of the Golgi and other compartments of the secretory pathway offered to us through EM have helped to inspire the development and application of some of our most informative, complimentary (molecular, biochemical and genetic) approaches. Even so, no one has yet even come close to relating the basic molecular mechanisms of transport, through and from the Golgi, to its ultrastructure, to everybody's satisfaction. Over the past decade, EM tomography has afforded new insights into structure-function relationships of the Golgi and provoked a re-evaluation of older paradigms. By providing a set of tools for structurally dissecting cells at high-resolution in three-dimensions (3D), EM tomography has emerged as a method for studying molecular cell biology in situ. As we move rapidly toward the establishment of molecular atlases of organelles through advances in proteomics and genomics, tomographic studies of the Golgi offer the tantalizing possibility that one day, we will be able to map the spatio-temporal coordinates of Golgi-related proteins and lipids accurately in the context of 4D cellular space.
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Affiliation(s)
- Brad J Marsh
- Institute for Molecular Bioscience, Centre for Microscopy and Microanalysis, and School of Molecular and Microbial Sciences, The University of Queensland, St. Lucia QLD 4072, Australia.
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263
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Loo JA, Berhane B, Kaddis CS, Wooding KM, Xie Y, Kaufman SL, Chernushevich IV. Electrospray ionization mass spectrometry and ion mobility analysis of the 20S proteasome complex. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:998-1008. [PMID: 15914020 DOI: 10.1016/j.jasms.2005.02.017] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2004] [Revised: 02/14/2005] [Accepted: 02/14/2005] [Indexed: 05/02/2023]
Abstract
Mass spectrometry and gas phase ion mobility [gas phase electrophoretic macromolecule analyzer (GEMMA)] with electrospray ionization were used to characterize the structure of the noncovalent 28-subunit 20S proteasome from Methanosarcina thermophila and rabbit. ESI-MS measurements with a quadrupole time-of-flight analyzer of the 192 kDa alpha7-ring and the intact 690 kDa alpha7beta7beta7alpha7 are consistent with their expected stoichiometries. Collisionally activated dissociation of the 20S gas phase complex yields loss of individual alpha-subunits only, and it is generally consistent with the known alpha7beta7beta7alpha7 architecture. The analysis of the binding of a reversible inhibitor to the 20S proteasome shows the expected stoichiometry of one inhibitor for each beta-subunit. Ion mobility measurements of the alpha7-ring and the alpha7beta7beta7alpha7 complex yield electrophoretic diameters of 10.9 and 15.1 nm, respectively; these dimensions are similar to those measured by crystallographic methods. Sequestration of multiple apo-myoglobin substrates by a lactacystin-inhibited 20S proteasome is demonstrated by GEMMA experiments. This study suggests that many elements of the gas phase structure of large protein complexes are preserved upon desolvation, and that methods such as mass spectrometry and ion mobility analysis can reveal structural details of the solution protein complex.
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Affiliation(s)
- Joseph A Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095-1570, USA.
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264
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Wei Z, Song J. Molecular mechanism underlying the thermal stability and pH-induced unfolding of CHABII. J Mol Biol 2005; 348:205-18. [PMID: 15808864 DOI: 10.1016/j.jmb.2005.02.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 02/14/2005] [Accepted: 02/15/2005] [Indexed: 10/25/2022]
Abstract
The 37-residue alpha/beta protein CHABII was previously demonstrated to undergo a gradual pH-induced unfolding. It has been shown that even at pH 4.0 CHABII still retained a highly native-like secondary structure and tertiary topology although its tight side-chain packing was severely disrupted, typical of the molten globule state. Here, we have expressed and refolded the recombinant proteins of CHABII and its mutant [Phe21]-CHABII, and subsequently conducted extensive CD and NMR characterizations. The results indicated: (1) replacement of His21 by Phe in [Phe21]-CHABII eliminated the pH-induced unfolding from pH 6.5 to 4.0, indicating that His21 was responsible for the observed pH-induced unfolding of CHABII. Further examinations revealed that although the pH-induced unfolding of CHABII was also triggered by the protonation of the His residue as previously uncovered for apomyoglobin, their molecular mechanisms are different. (2) Monitoring the pH-induced unfolding by 1H-15N HSQC spectroscopy allowed us to visualize the gradual development of the CHABII molten globule. At pH 4.0, the HSQC spectrum of CHABII was poorly dispersed with dispersions of approximately 1 ppm over proton dimension and 10 ppm over 15N dimension, characteristic of severely or even "completely unfolded" proteins. One the other hand, unambiguous assignments of the NOESY spectra of CHABII led to the identification of the persistent medium and long-range NOEs at pH 4.0, which define a highly native-like secondary structure and tertiary packing. This implies that the degree of the native-like topology might be underestimated in the previous characterization of partially folded and even completely unfolded proteins. (3) Replacement of His21 by Phe with higher side-chain hydrophobicity only caused a minor structural rearrangement but considerably enhanced the packing interaction of the hydrophobic core, as evident from a dramatic increase in NOE contacts in [Phe21]-CHABII. The enhancement led to an increase of the thermal stability of [Phe21]-CHABII by approximately 17 deg. C.
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Affiliation(s)
- Zheng Wei
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge, Crescent, Singapore 119260
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265
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Högbom M, Ericsson UB, Lam R, Bakali H MA, Kuznetsova E, Nordlund P, Zamble DB. A High Throughput Method for the Detection of Metalloproteins on a Microgram Scale. Mol Cell Proteomics 2005; 4:827-34. [PMID: 15772113 DOI: 10.1074/mcp.t400023-mcp200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteins that bind transition metals make up a substantial portion of the proteome, and the identification of a metal cofactor in a protein can greatly facilitate its functional assignment and help place it in the context of known cellular pathways. Existing methods for the detection of metalloproteins generally consume large amounts of protein, require expensive equipment, or are very labor intensive, rendering them unsuitable for use in high throughput proteomic initiatives. Here we present a method for the identification of metalloproteins that contain iron, copper, manganese, cobalt, nickel, and/or zinc that is sensitive, quick, robust, inexpensive, and can be performed with standard laboratory equipment. The assay is based on a combination of chemiluminescence and colorimetric detection methods, it typically consumes only 10 microg of protein, and most common chemical components of protein solutions do not interfere with metal detection. Analysis of 52 protein samples was compared with the results from inductively coupled plasma-atomic emission spectrometry to verify the accuracy and sensitivity of the method. The assay is conducted in a 384-well format and requires about 3 h for completion, including a 2-h wait; so whole proteomes can be assayed for metal content in a matter of days.
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Affiliation(s)
- Martin Högbom
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
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266
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Petoukhov MV, Svergun DI. Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys J 2005; 89:1237-50. [PMID: 15923225 PMCID: PMC1366608 DOI: 10.1529/biophysj.105.064154] [Citation(s) in RCA: 738] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
New methods to automatically build models of macromolecular complexes from high-resolution structures or homology models of their subunits or domains against x-ray or neutron small-angle scattering data are presented. Depending on the complexity of the object, different approaches are employed for the global search of the optimum configuration of subunits fitting the experimental data. An exhaustive grid search is used for hetero- and homodimeric particles and for symmetric oligomers formed by identical subunits. For the assemblies or multidomain proteins containing more then one subunit/domain per asymmetric unit, heuristic algorithms based on simulated annealing are used. Fast computational algorithms based on spherical harmonics representation of scattering amplitudes are employed. The methods allow one to construct interconnected models without steric clashes, to account for the particle symmetry and to incorporate information from other methods, on distances between specific residues or nucleotides. For multidomain proteins, addition of missing linkers between the domains is possible. Simultaneous fitting of multiple scattering patterns from subcomplexes or deletion mutants is incorporated. The efficiency of the methods is illustrated by their application to complexes of different types in several simulated and practical examples. Limitations and possible ambiguity of rigid body modeling are discussed and simplified docking criteria are provided to rank multiple models. The methods described are implemented in publicly available computer programs running on major hardware platforms.
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267
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Liu HL, Hsu JP. Recent developments in structural proteomics for protein structure determination. Proteomics 2005; 5:2056-68. [PMID: 15846841 DOI: 10.1002/pmic.200401104] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The major challenges in structural proteomics include identifying all the proteins on the genome-wide scale, determining their structure-function relationships, and outlining the precise three-dimensional structures of the proteins. Protein structures are typically determined by experimental approaches such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. However, the knowledge of three-dimensional space by these techniques is still limited. Thus, computational methods such as comparative and de novo approaches and molecular dynamic simulations are intensively used as alternative tools to predict the three-dimensional structures and dynamic behavior of proteins. This review summarizes recent developments in structural proteomics for protein structure determination; including instrumental methods such as X-ray crystallography and NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulations.
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Affiliation(s)
- Hsuan-Liang Liu
- Department of Chemical Engineering, National Taipei University of Technology, Taiwan.
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268
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Leong PA, Heymann JB, Jensen GJ. Peach: A Simple Perl-Based System for Distributed Computation and Its Application to Cryo-EM Data Processing. Structure 2005; 13:505-11. [PMID: 15837189 DOI: 10.1016/j.str.2005.01.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Revised: 01/12/2005] [Accepted: 01/14/2005] [Indexed: 10/25/2022]
Abstract
A simple distributed processing system named "Peach" was developed to meet the rising computational demands of modern structural biology (and other) laboratories without additional expense by using existing hardware resources more efficiently. A central server distributes jobs to idle workstations in such a way that each computer is used maximally, but without disturbing intermittent interactive users. As compared to other distributed systems, Peach is simple, easy to install, easy to administer, easy to use, scalable, and robust. While it was designed to queue and distribute large numbers of small tasks to participating computers, it can also be used to send single jobs automatically to the fastest currently available computer and/or survey the activity of an entire laboratory's computers. Tests of robustness and scalability are reported, as are three specific electron cryomicroscopy applications where Peach enabled projects that would not otherwise have been feasible without an expensive, dedicated cluster.
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Affiliation(s)
- Peter A Leong
- Department of Applied Physics, California Institute of Technology, 1200 E. California Boulevard, Pasadena, California 91125, USA
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269
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Baumeister W. From proteomic inventory to architecture. FEBS Lett 2005; 579:933-7. [PMID: 15680977 DOI: 10.1016/j.febslet.2004.10.102] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2004] [Accepted: 10/29/2004] [Indexed: 12/20/2022]
Abstract
Electron tomography can provide three-dimensional reconstructions of large pleomorphic structures at molecular resolution. While the principles of electron tomography have been known for decades, its use has gathered momentum only in recent years. Technological advances have made it possible to apply it to ice-embedded biological material (cryotomography), thereby ensuring a close-to-life preservation of the samples. In combination with advanced computational methods, such as molecular identification based on pattern recognition, it is a promising approach to comprehensively map macromolecular architecture inside organelles and cells and to visualize macromolecules at work in their natural environment.
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Affiliation(s)
- Wolfgang Baumeister
- Department of Structural Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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270
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Abstract
Previous studies have suggested that nature is restricted to about 1,000 protein folds to perform a great diversity of functions. Here, we use protein interaction data from different sources and three-dimensional structures to suggest that the total number of interaction types is also limited, and estimate that most interactions in nature will conform to one of about 10,000 types. We currently know fewer than 2,000, and at the present rate of structure determination, it will be more than 20 years before we know a full representative set.
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Affiliation(s)
- Patrick Aloy
- EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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271
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Benjamin J, Ganser-Pornillos BK, Tivol WF, Sundquist WI, Jensen GJ. Three-dimensional structure of HIV-1 virus-like particles by electron cryotomography. J Mol Biol 2005; 346:577-88. [PMID: 15670606 PMCID: PMC6608732 DOI: 10.1016/j.jmb.2004.11.064] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Revised: 11/18/2004] [Accepted: 11/23/2004] [Indexed: 11/22/2022]
Abstract
While the structures of nearly every HIV-1 protein are known in atomic detail from X-ray crystallography and NMR spectroscopy, many questions remain about how the individual proteins are arranged in the mature infectious viral particle. Here, we report the three-dimensional structures of individual HIV-1 virus-like particles (VLPs) as obtained by electron cryotomography. These reconstructions revealed that while the structures and positions of the conical cores within each VLP were unique, they exhibited several surprisingly consistent features, including similarities in the size and shape of the wide end of the capsid (the "base"), uniform positioning of the base and other regions of the capsid 11nm away from the envelope/MA layer, a cone angle that typically varied from 24 degrees to 18 degrees around the long axis of the cone, and an internal density (presumably part of the NC/RNA complex) cupped within the base. Multiple and nested capsids were observed. These results support the fullerene cone model for the viral capsid, indicate that viral maturation involves a free re-organization of the capsid shell rather than a continuous condensation, imply that capsid assembly is both concentration-driven and template-driven, suggest that specific interactions exist between the capsid and the adjacent envelope/MA and NC/RNA layers, and show that a particular capsid shape is favored strongly in-vivo.
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Affiliation(s)
- Jordan Benjamin
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena CA 91125, USA
| | | | - William F. Tivol
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena CA 91125, USA
| | - Wesley I. Sundquist
- Department of Biochemistry University of Utah School of Medicine, 20 N, 1900 E, Salt Lake City, UT 84132-3201 USA
| | - Grant J. Jensen
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena CA 91125, USA
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272
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Heymann JB, Conway JF, Steven AC. Molecular dynamics of protein complexes from four-dimensional cryo-electron microscopy. J Struct Biol 2005; 147:291-301. [PMID: 15450298 DOI: 10.1016/j.jsb.2004.02.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Revised: 02/04/2004] [Indexed: 11/23/2022]
Abstract
Cryo-electron microscopy of single particles offers a unique opportunity to detect and quantify conformational variation of protein complexes. Different conformers may, in principle, be distinguished by classification of individual projections in which image differences arising from viewing geometry are disentangled from variability in the underlying structures by "multiple particle analysis"--MPA. If the various conformers represent dynamically related states of the same complex, MPA has the potential to visualize transition states, and eventually to yield movies of the dynamic process. Ordering the various conformers into a time series is facilitated if cryo-EM data are taken at successive times from a system that is known to be developing in time. Virus maturation represents a relatively tractable dynamic process because the changes are large and irreversible and the rate of the natural process may be conveniently slowed in vitro by adjusting the environmental conditions. We describe the strategy employed in a recent analysis of herpes simplex virus procapsid maturation (Nat. Struct. Biol. 10 (2003) 334-341), compare it with previous work on the maturation of bacteriophage HK97 procapsid, and discuss various factors that impinge on the feasibility of performing similar experimental analyses of molecular dynamics in the general case.
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Affiliation(s)
- J Bernard Heymann
- Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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273
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Topf M, Baker ML, John B, Chiu W, Sali A. Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J Struct Biol 2005; 149:191-203. [PMID: 15681235 DOI: 10.1016/j.jsb.2004.11.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2004] [Revised: 11/05/2004] [Indexed: 02/01/2023]
Abstract
We explore structural characterization of protein assemblies by a combination of electron cryo-microscopy (cryoEM) and comparative protein structure modeling. Specifically, our method finds an optimal atomic model of a given assembly subunit and its position within an assembly by fitting alternative comparative models into a cryoEM map. The alternative models are calculated by MODELLER [J. Mol. Biol. 234 (1993) 313] from different sequence alignments between the modeled protein and its template structures. The fitting of these models into a cryoEM density map is performed either by FOLDHUNTER [J. Mol. Biol. 308 (2001) 1033] or by a new density fitting module of MODELLER (Mod-EM). Identification of the most accurate model is based on the correlation between the model accuracy and the quality of fit into the cryoEM density map. To quantify this correlation, we created a benchmark consisting of eight proteins of different structural folds with corresponding density maps simulated at five resolutions from 5 to 15 angstroms, with three noise levels each. Each of the proteins in the set was modeled based on 300 different alignments to their remotely related templates (12-32% sequence identity), spanning the range from entirely inaccurate to essentially accurate alignments. The benchmark revealed that one of the most accurate models can usually be identified by the quality of its fit into the cryoEM density map, even for noisy maps at 15 angstroms resolution. Therefore, a cryoEM density map can be helpful in improving the accuracy of a comparative model. Moreover, a pseudo-atomic model of a component in an assembly may be built better with comparative models of the native subunit sequences than with experimentally determined structures of their homologs.
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Affiliation(s)
- Maya Topf
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California, San Francisco, CA 94143, USA
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274
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Abstract
MOTIVATION In recent years, the Protein Data Bank (PDB) has experienced rapid growth. To maximize the utility of the high resolution protein-protein interaction data stored in the PDB, we have developed PIBASE, a comprehensive relational database of structurally defined interfaces between pairs of protein domains. It is composed of binary interfaces extracted from structures in the PDB and the Probable Quaternary Structure server using domain assignments from the Structural Classification of Proteins and CATH fold classification systems. RESULTS PIBASE currently contains 158,915 interacting domain pairs between 105,061 domains from 2125 SCOP families. A diverse set of geometric, physiochemical and topologic properties are calculated for each complex, its domains, interfaces and binding sites. A subset of the interface properties are used to remove interface redundancy within PDB entries, resulting in 20,912 distinct domain-domain interfaces. The complexes are grouped into 989 topological classes based on their patterns of domain-domain contacts. The binary interfaces and their corresponding binding sites are categorized into 18,755 and 30,975 topological classes, respectively, based on the topology of secondary structure elements. The utility of the database is illustrated by outlining several current applications. AVAILABILITY The database is accessible via the world wide web at http://salilab.org/pibase SUPPLEMENTARY INFORMATION http://salilab.org/pibase/suppinfo.html.
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Affiliation(s)
- Fred P Davis
- Graduate Group in Biophysics, California Institute for Quantitative Biomedical Research, University of California, San Francisco, 94143, USA
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275
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Martin DC, Chen J, Yang J, Drummy LF, Kübel C. High resolution electron microscopy of ordered polymers and organic molecular crystals: Recent developments and future possibilities. ACTA ACUST UNITED AC 2005. [DOI: 10.1002/polb.20419] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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276
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Fritzsche PC, Fernández JJ, Ripoll A, García I, Luque E. A Performance Prediction Model for Tomographic Reconstruction in Structural Biology. ACTA ACUST UNITED AC 2005. [DOI: 10.1007/11403937_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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277
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Affiliation(s)
- Wolfgang Baumeister
- Department of Structural Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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278
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279
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280
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Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. A structural perspective on protein-protein interactions. Curr Opin Struct Biol 2004; 14:313-24. [PMID: 15193311 DOI: 10.1016/j.sbi.2004.04.006] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Structures of macromolecular complexes are necessary for a mechanistic description of biochemical and cellular processes. They can be solved by experimental methods, such as X-ray crystallography, NMR spectroscopy and electron microscopy, as well as by computational protein structure prediction, docking and bioinformatics. Recent advances and applications of these methods emphasize the need for hybrid approaches that combine a variety of data to achieve better efficiency, accuracy, resolution and completeness.
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281
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Abstract
Comparison of two protein structures often results in not only a global alignment but also a number of distinct local alignments; the latter, referred to as alternative alignments, are however usually ignored in existing protein structure comparison analyses. Here, we used a novel method of protein structure comparison to extensively identify and characterize the alternative alignments obtained for structure pairs of a fold classification database. We showed that all alternative alignments can be classified into one of just a few types, and with which illustrated the potential of using alternative alignments to identify recurring protein substructures, including the internal structural repeats of a protein. Furthermore, we showed that among the alternative alignments obtained, permuted alignments, which included both circular and scrambled permutations, are as prevalent as topological alignments. These results demonstrated that the so far largely unattended alternative alignments of protein structures have implications and applications for research of protein classification and evolution.
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Affiliation(s)
- Edward S C Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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282
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Zhao Q, Ofverstedt LG, Skoglund U, Isaksson LA. Morphological variation of individual Escherichia coli 50S ribosomal subunits in situ, as revealed by cryo-electron tomography. Exp Cell Res 2004; 300:190-201. [PMID: 15383326 DOI: 10.1016/j.yexcr.2004.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2004] [Revised: 07/08/2004] [Indexed: 10/26/2022]
Abstract
Electron tomography (ET) has been used to reconstruct in situ individual 50S ribosomal subunits in Escherichia coli rifampicin-treated cells. Rifampicin inhibits transcription initiation. As a result, rapid degradation of preformed mRNA and dissociation of 70S ribosomes give accumulation of free subunits. In the 50S subunit, the L1 stalk, the L7/L12 stalk, the central protuberance (CP), and the peptidyl transferase center (PTC) cleft are the most dynamic and flexible parts in the reconstructed structures with clear movements indicated. Different locations of the tunnel in the central cross-sections through the in situ 50S subunits indicate the flexible nature of the pathway inside the large ribosomal subunit. In addition, gross morphological heterogeneity was observed in the reconstructions. Our results demonstrate a considerable structural variability among individual 50S subunits in the intracellular environment.
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Affiliation(s)
- Qing Zhao
- Department of Genetics, Microbiology and Toxicology, Stockholm University, S-106 91 Stockholm, Sweden
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283
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Atanassova A, Lam R, Zamble DB. A high-performance liquid chromatography method for determining transition metal content in proteins. Anal Biochem 2004; 335:103-11. [PMID: 15519577 DOI: 10.1016/j.ab.2004.08.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Indexed: 01/12/2023]
Abstract
Transition metals are common components of cellular proteins and the detailed study of metalloproteins necessitates the identification and quantification of bound metal ions. Screening for metals is also an informative step in the initial characterization of the numerous unknown and unclassified proteins now coming through the proteomic pipeline. We have developed a high-performance liquid chromatography method for the quantitative determination of the most prevalent biological transition metals: manganese, iron, cobalt, nickel, copper, and zinc. The method is accurate and simple and can be adapted for automated high-throughput studies. The metal analysis involves acid hydrolysis to release the metal ions into solution, followed by ion separation on a mixed-bead ion-exchange column and absorbance detection after postcolumn derivatization with the metallochromic indicator 4-(2-pyridylazo)resorcinol. The potential interferences by common components of protein solutions were investigated. The metal content of a variety of metalloproteins was analyzed and the data were compared to data obtained from inductively coupled plasma-atomic emission spectroscopy. The sensitivity of the assay allows for the detection of 0.1-0.8 nmol, depending on the metal. The amount of protein required is governed by the size of the protein and the fraction of protein with metal bound. For routine analysis 50 microg was used but for many proteins 10 microg would be sufficient. The advantages, disadvantages, and possible applications of this method are discussed.
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Affiliation(s)
- Anelia Atanassova
- Department of Chemistry, University of Toronto, Lash Miller Chemical Laboratories, 80 St. George St., Toronto, Ont., Canada M5S 3H6
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284
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Vasilescu J, Guo X, Kast J. Identification of protein-protein interactions usingin vivo cross-linking and mass spectrometry. Proteomics 2004; 4:3845-54. [PMID: 15540166 DOI: 10.1002/pmic.200400856] [Citation(s) in RCA: 182] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The purification of protein complexes can be accomplished by different types of affinity chromatography. In a typical immunoaffinity experiment, protein complexes are captured from a cell lysate by an immobilized antibody that recognizes an epitope on one of the known components of the complex. After extensive washing to remove unspecifically bound proteins, the complexes are eluted and analyzed by mass spectrometry (MS). Transient complexes, which are characterized by high dissociation constants, are typically lost by this approach. In the present study, we describe a novel method for identifying transient protein-protein interactions using in vivo cross-linking and MS-based protein identification. Live cells are treated with formaldehyde, which rapidly permeates the cell membrane and generates protein-protein cross-links. Proteins cross-linked to a Myc-tagged protein of interest are copurified by immunoaffinity chromatography and subjected to a procedure which dissociates the cross-linked complexes. After separation by SDS-PAGE, proteins are identified by tandem mass spectrometry. Application of this method enabled the identification of numerous proteins that copurified with a constitutively active form of M-Ras (M-Ras(Q71L)). Among these, we identified the RasGAP-related protein IQGAP1 to be a novel interaction partner of M-Ras(Q71L). This method is applicable to many proteins and will aid in the study of protein-protein interactions.
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Affiliation(s)
- Julian Vasilescu
- The Biomedical Research Centre, University of British Columbia, Vancouver, Canada
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285
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Pajon A, Ionides J, Diprose J, Fillon J, Fogh R, Ashton AW, Berman H, Boucher W, Cygler M, Deleury E, Esnouf R, Janin J, Kim R, Krimm I, Lawson CL, Oeuillet E, Poupon A, Raymond S, Stevens T, van Tilbeurgh H, Westbrook J, Wood P, Ulrich E, Vranken W, Xueli L, Laue E, Stuart DI, Henrick K. Design of a data model for developing laboratory information management and analysis systems for protein production. Proteins 2004; 58:278-84. [PMID: 15562521 DOI: 10.1002/prot.20303] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Data management has emerged as one of the central issues in the high-throughput processes of taking a protein target sequence through to a protein sample. To simplify this task, and following extensive consultation with the international structural genomics community, we describe here a model of the data related to protein production. The model is suitable for both large and small facilities for use in tracking samples, experiments, and results through the many procedures involved. The model is described in Unified Modeling Language (UML). In addition, we present relational database schemas derived from the UML. These relational schemas are already in use in a number of data management projects.
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Affiliation(s)
- Anne Pajon
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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286
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Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N. High-throughput computational and experimental techniques in structural genomics. Genome Res 2004; 14:2145-54. [PMID: 15489337 PMCID: PMC528931 DOI: 10.1101/gr.2537904] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Structural genomics has as its goal the provision of structural information for all possible ORF sequences through a combination of experimental and computational approaches. The access to genome sequences and cloning resources from an ever-widening array of organisms is driving high-throughput structural studies by the New York Structural Genomics Research Consortium. In this report, we outline the progress of the Consortium in establishing its pipeline for structural genomics, and some of the experimental and bioinformatics efforts leading to structural annotation of proteins. The Consortium has established a pipeline for structural biology studies, automated modeling of ORF sequences using solved (template) structures, and a novel high-throughput approach (metallomics) to examining the metal binding to purified protein targets. The Consortium has so far produced 493 purified proteins from >1077 expression vectors. A total of 95 have resulted in crystal structures, and 81 are deposited in the Protein Data Bank (PDB). Comparative modeling of these structures has generated >40,000 structural models. We also initiated a high-throughput metal analysis of the purified proteins; this has determined that 10%-15% of the targets contain a stoichiometric structural or catalytic transition metal atom. The progress of the structural genomics centers in the U.S. and around the world suggests that the goal of providing useful structural information on most all ORF domains will be realized. This projected resource will provide structural biology information important to understanding the function of most proteins of the cell.
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Affiliation(s)
- Mark R Chance
- New York Structural Genomics Research Consortium, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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287
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Abstract
The APC (anaphase-promoting complex) is a multisubunit E3 ubiquitin ligase that targets cell-cycle-related proteins for degradation by the 26 S proteasome. The APC contains at least 13 subunits and is regulated by the binding of co-activator proteins and by phosphorylation. It is not known why the APC contains 13 subunits when many other ubiquitin ligases are small single-subunit enzymes. In the present study, the structures and functions of individual APC subunits are discussed. By dissecting the roles of its parts, we hope to gain insight into the mechanism of the intact APC.
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Affiliation(s)
- L A Passmore
- Section of Structural Biology, Chester Beatty Laboratories, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
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288
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Abstract
Proteomics is an increasingly powerful and indispensable technology in molecular cell biology. It can be used to identify the components of small protein complexes and large organelles, to determine post-translational modifications and in sophisticated functional screens. The key - but little understood - technology in mass-spectrometry-based proteomics is peptide sequencing, which we describe and review here in an easily accessible format.
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Affiliation(s)
- Hanno Steen
- Department of Systems Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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289
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Xia Y, Yu H, Jansen R, Seringhaus M, Baxter S, Greenbaum D, Zhao H, Gerstein M. Analyzing cellular biochemistry in terms of molecular networks. Annu Rev Biochem 2004; 73:1051-87. [PMID: 15189167 DOI: 10.1146/annurev.biochem.73.011303.073950] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
One way to understand cells and circumscribe the function of proteins is through molecular networks. These networks take a variety of forms including webs of protein-protein interactions, regulatory circuits linking transcription factors and targets, and complex pathways of metabolic reactions. We first survey experimental techniques for mapping networks (e.g., the yeast two-hybrid screens). We then turn our attention to computational approaches for predicting networks from individual protein features, such as correlating gene expression levels or analyzing sequence coevolution. All the experimental techniques and individual predictions suffer from noise and systematic biases. These problems can be overcome to some degree through statistical integration of different experimental datasets and predictive features (e.g., within a Bayesian formalism). Next, we discuss approaches for characterizing the topology of networks, such as finding hubs and analyzing subnetworks in terms of common motifs. Finally, we close with perspectives on how network analysis represents a preliminary step toward a systems approach for modeling cells.
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Affiliation(s)
- Yu Xia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
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290
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Abstract
Traditional textbook representations of the prokaryotic cytoplasm show an amorphous, unstructured amalgamation of proteins and small molecules in which a randomly arranged chromosome resides. The development and application of a swathe of microscopic techniques over the last 10 years in particular, has shown this image of the microbial cell to be incorrect: the cytoplasm is highly structured with many proteins carrying out their assigned functions at specific subcellular locations; bacteria contain cytoskeletal elements including microtubule, actin and intermediate filament homologues; the chromosome is not randomly folded and is organized in such a way as to facilitate efficient segregation upon cell division. This review will concentrate on recent advances in our understanding of subcellular architecture and the techniques that have led to these discoveries.
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Affiliation(s)
- Peter J Lewis
- School of Environmental and Life Sciences, Biological Sciences, University of Newcastle, Callaghan, NSW 2308, Australia.
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291
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Abstract
AbstractCryoelectron tomography opens a window into the inner space of cells. It combines the potential of three-dimensional imaging with a close-to-life preservation of biological samples. Tomograms with molecular resolution are essentially images of the cellular proteome and, in conjunction with advanced pattern recognition techniques, they can be used to map the molecular landscape inside organelles and cells.
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Affiliation(s)
- Wolfgang Baumeister
- Department of Structural Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.
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292
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Banyay M, Gilstring F, Hauzenberger E, Ofverstedt LG, Eriksson AB, Krupp JJ, Larsson O. Three-Dimensional Imaging of In Situ Specimens with Low-Dose Electron Tomography to Analyze Protein Conformation. Assay Drug Dev Technol 2004; 2:561-7. [PMID: 15671654 DOI: 10.1089/adt.2004.2.561] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We describe a novel three-dimensional (3-D) imaging tool for analysis of protein conformation of in situ samples. Sidec (Sidec Technologies AB, Stockholm, Sweden) electron tomography (SET) uses low-dose electron tomography and a refinement algorithm to reconstruct individual proteins and macromolecular complexes. The approach has successfully reconstructed therapeutic proteins in solution. In this study, we investigate the use of SET to visualize ion channels in cells and tissue samples. SET successfully resolved the volume and structural features of the target complex, showing that it was a tetrameric channel with a central pore. The technology could distinguish and provide 3-D images of the intra- and extracellular domains in the ion channel. In addition, SET was able to show that the channel associates in the form of a tetramer with the four subunits preorganized into dimers. While additional studies using smaller antibody markers are needed to resolve the subunit assembly further, this study demonstrates that SET is a valuable tool for visualization of in situ specimens and can provide important information on the subunit assembly of these macromolecular complexes, and thereby aid in the screening assay process in drug development.
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Affiliation(s)
- Martina Banyay
- Sidec Technologies AB, Fogdevreten 2A, SE-17177 Stockholm, Sweden
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293
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Abstract
The genome sequences of important model systems are available and the focus is now shifting to large-scale experiments enabled by this data. Following in the footsteps of genomics, we have functional genomics, proteomics, and even metabolomics, roughly paralleling the biological hierarchy of the transcription, translation, and production of small molecules. Proteomics is initially concerned with determining the structure, expression, localization, biochemical activity, interactions, and cellular roles of as many proteins as possible. There has been great progress owing to novel instrumentation, experimental strategies, and bioinformatics methods. The area of protein-protein interactions has been especially fruitful. First pass interaction maps of some model organisms exist, and the proteins in many important organelles are about to be determined. Researchers are also beginning to integrate large-scale data sets from various "omics" disciplines in targeted investigations of specific biomedical areas and in pursuit of a general framework for systems biology.
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Affiliation(s)
- Carmen L de Hoog
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark.
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294
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Huang K, Murphy RF. From quantitative microscopy to automated image understanding. JOURNAL OF BIOMEDICAL OPTICS 2004; 9:893-912. [PMID: 15447010 PMCID: PMC1458526 DOI: 10.1117/1.1779233] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Quantitative microscopy has been extensively used in biomedical research and has provided significant insights into structure and dynamics at the cell and tissue level. The entire procedure of quantitative microscopy is comprised of specimen preparation, light absorption/reflection/emission from the specimen, microscope optical processing, optical/electrical conversion by a camera or detector, and computational processing of digitized images. Although many of the latest digital signal processing techniques have been successfully applied to compress, restore, and register digital microscope images, automated approaches for recognition and understanding of complex subcellular patterns in light microscope images have been far less widely used. We describe a systematic approach for interpreting protein subcellular distributions using various sets of subcellular location features (SLF), in combination with supervised classification and unsupervised clustering methods. These methods can handle complex patterns in digital microscope images, and the features can be applied for other purposes such as objectively choosing a representative image from a collection and performing statistical comparisons of image sets.
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Affiliation(s)
- Kai Huang
- Departments of Biological Sciences and Biomedical Engineering and Center for Automated Learning and Discovery Carnegie Mellon University 4400 Fifth Avenue, Pittsburgh PA 15213 Phone: 1.412.268.3480 FAX: 1.412.268.6571
| | - Robert F. Murphy
- Departments of Biological Sciences and Biomedical Engineering and Center for Automated Learning and Discovery Carnegie Mellon University 4400 Fifth Avenue, Pittsburgh PA 15213 Phone: 1.412.268.3480 FAX: 1.412.268.6571
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295
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Al-Amoudi A, Chang JJ, Leforestier A, McDowall A, Salamin LM, Norlén LPO, Richter K, Blanc NS, Studer D, Dubochet J. Cryo-electron microscopy of vitreous sections. EMBO J 2004; 23:3583-8. [PMID: 15318169 PMCID: PMC517607 DOI: 10.1038/sj.emboj.7600366] [Citation(s) in RCA: 329] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2004] [Accepted: 07/23/2004] [Indexed: 11/09/2022] Open
Abstract
Since the beginning of the 1980s, cryo-electron microscopy of a thin film of vitrified aqueous suspension has made it possible to observe biological particles in their native state, in the absence of the usual artefacts of dehydration and staining. Combined with 3-d reconstruction, it has become an important tool for structural molecular biology. Larger objects such as cells and tissues cannot generally be squeezed in a thin enough film. Cryo-electron microscopy of vitreous sections (CEMOVIS) provides then a solution. It requires vitrification of a sizable piece of biological material and cutting it into ultrathin sections, which are observed in the vitrified state. Each of these operations raises serious difficulties that have now been overcome. In general, the native state seen with CEMOVIS is very different from what has been seen before and it is seen in more detail. CEMOVIS will give its full potential when combined with computerized electron tomography for 3-d reconstruction.
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Affiliation(s)
- Ashraf Al-Amoudi
- Laboratoire d'Analyse Ultrastructurale, Bâtiment de Biologie, Université de Lausanne, Lausanne, Switzerland
| | - Jiin-Ju Chang
- Institute of Biophysics, Academy of Sciences, Beijing, China
| | - Amélie Leforestier
- Laboratoire de Physique des Solides, CNRS URA002, Université Paris-Sud, Orsay, France
| | - Alasdair McDowall
- Centre for Microscopy and Microanalysis, University of Queensland, St Lucia, Australia
| | - Laurée Michel Salamin
- Laboratoire d'Analyse Ultrastructurale, Bâtiment de Biologie, Université de Lausanne, Lausanne, Switzerland
| | - Lars P O Norlén
- Groupe de Physique appliquée, Departement de physique, Université de Genève, Genève, Switzerland
| | | | - Nathalie Sartori Blanc
- Laboratoire d'Analyse Ultrastructurale, Bâtiment de Biologie, Université de Lausanne, Lausanne, Switzerland
| | | | - Jacques Dubochet
- Laboratoire d'Analyse Ultrastructurale, Bâtiment de Biologie, Université de Lausanne, Lausanne, Switzerland
- Laboratoire d'Analyse Ultrastructurale, Bâtiment de Biologie, Université de Lausanne, 1015 Lausanne, Switzerland. Tel.: +41 21 692 42 80; Fax: +41 21 692 41 05; E-mail:
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296
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Abstract
During the past decade, enormous advances have been made in cell biology. Major advances included the publication of the human genome sequence, the development of proteomics, and DNA microarray technologies and techniques to selectively "silence" genes using short strands of double-stranded RNA. Some areas of great progress that are particularly relevant to critical care medicine include huge improvements in our understanding of the signal transduction pathways involved in the innate immune response and adaptation to hypoxia. Other areas of important progress include improvements in our understanding of how inflammation causes derangements in epithelial structure and function and impairs cellular utilization of oxygen.
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Affiliation(s)
- Mitchell P Fink
- Departments of Critical Care Medicine and Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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297
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Fernández JJ, Li S. An improved algorithm for anisotropic nonlinear diffusion for denoising cryo-tomograms. J Struct Biol 2004; 144:152-61. [PMID: 14643218 DOI: 10.1016/j.jsb.2003.09.010] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cryo-electron tomography is an imaging technique with an unique potential for visualizing large complex biological specimens. It ensures preservation of the biological material but the resulting cryotomograms are extremely noisy. Sophisticated denoising techniques are thus essential for allowing the visualization and interpretation of the information contained in the cryotomograms. Here a software tool based on anisotropic nonlinear diffusion is described for filtering cryotomograms. The approach reduces local noise and meanwhile enhances both curvilinear and planar structures. In the program a novel solution of the partial differential equation has been implemented, which allows a reliable estimation of derivatives and, furthermore, reduces computation time and memory requirements. Several criteria have been included to automatically select the optimal stopping time. The behaviour of the denoising approach is tested for visualizing filamentous structures in cryotomograms.
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Affiliation(s)
- José Jesús Fernández
- Department of Computer Architecture and Electronics, University of Almería, 04120 Almería, Spain.
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298
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Abstract
Understanding the molecular function of proteins is greatly enhanced by insights gained from their three-dimensional structures. Since experimental structures are only available for a small fraction of proteins, computational methods for protein structure modeling play an increasingly important role. Comparative protein structure modeling is currently the most accurate method, yielding models suitable for a wide spectrum of applications, such as structure-guided drug development or virtual screening. Stable and reliable automated prediction pipelines have been developed to apply large-scale comparative modeling to whole genomes or entire sequence databases. Model repositories give access to these annotated and evaluated models. In this review, we will discuss recent developments in automated comparative modeling and provide selected examples illustrating the use of homology models.
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Affiliation(s)
- Jurgen Kopp
- Biozentrum der Universitat Basel and Swiss Institute of Bioinformatics, Klingelbergstr. 50-70, CH 4056, Basel, Switzerland
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299
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300
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Frangakis AS, Förster F. Computational exploration of structural information from cryo-electron tomograms. Curr Opin Struct Biol 2004; 14:325-31. [PMID: 15193312 DOI: 10.1016/j.sbi.2004.04.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Cryo-electron tomography aims to act as an interface between in vivo cell imaging and techniques achieving atomic resolution. This attempt to bridge the resolution gap is facilitated by recent software and hardware advances. Information provided by atomically resolved macromolecules and molecular interaction data need to be put into a common framework in order to create a hybrid multidimensional cellular image. A major partner in this enterprise is the development of regularization and pattern recognition techniques, which try to identify macromolecular complexes as a function of their structural signature in cryo-electron tomograms of living cells.
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Affiliation(s)
- Achilleas S Frangakis
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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