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Bondos SE, Dunker AK, Uversky VN. On the roles of intrinsically disordered proteins and regions in cell communication and signaling. Cell Commun Signal 2021; 19:88. [PMID: 34461937 PMCID: PMC8404256 DOI: 10.1186/s12964-021-00774-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
For proteins, the sequence → structure → function paradigm applies primarily to enzymes, transmembrane proteins, and signaling domains. This paradigm is not universal, but rather, in addition to structured proteins, intrinsically disordered proteins and regions (IDPs and IDRs) also carry out crucial biological functions. For these proteins, the sequence → IDP/IDR ensemble → function paradigm applies primarily to signaling and regulatory proteins and regions. Often, in order to carry out function, IDPs or IDRs cooperatively interact, either intra- or inter-molecularly, with structured proteins or other IDPs or intermolecularly with nucleic acids. In this IDP/IDR thematic collection published in Cell Communication and Signaling, thirteen articles are presented that describe IDP/IDR signaling molecules from a variety of organisms from humans to fruit flies and tardigrades ("water bears") and that describe how these proteins and regions contribute to the function and regulation of cell signaling. Collectively, these papers exhibit the diverse roles of disorder in responding to a wide range of signals as to orchestrate an array of organismal processes. They also show that disorder contributes to signaling in a broad spectrum of species, ranging from micro-organisms to plants and animals.
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Affiliation(s)
- Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843, USA.
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Russia.
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2
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Chudapongse N, Krubphachaya P, Leelayuwat C, Kermode JC. Expression and Purification of a Soluble Recombinant A1 Domain of Human von Willebrand Factor in Bacteria. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2011.0087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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3
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Ostrowski J, Wyrwicz LS. Integrating genomics, proteomics and bioinformatics in translational studies of molecular medicine. Expert Rev Mol Diagn 2014; 9:623-30. [DOI: 10.1586/erm.09.41] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
High-throughput, automated or semiautomated methodologies implemented by companies and structural genomics initiatives have accelerated the process of acquiring structural information for proteins via x-ray crystallography. This has enabled the application of structure-based drug design technologies to a variety of new structures that have potential pharmacologic relevance. Although there remain major challenges to applying these approaches more broadly to all classes of drug discovery targets, clearly the continued development and implementation of these structure-based drug design methodologies by the scientific community at large will help to address and provide solutions to these hurdles. The result will be a growing number of protein structures of important pharmacologic targets that will help to streamline the process of identification and optimization of lead compounds for drug development. These lead agonist and antagonist pharmacophores should, in turn, help to alleviate one of the current critical bottlenecks in the drug discovery process; that is, defining the functional relevance of potential novel targets to disease modification. The prospect of generating an increasing number of potential drug candidates will serve to highlight perhaps the most significant future bottleneck for drug development, the cost and complexity of the drug approval process.
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Affiliation(s)
- Leslie W Tari
- ActiveSight, 4045 Sorrento Valley Blvd, San Diego, CA 92121, USA.
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5
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Tommy YBW, Lim TS, Noordin R, Saadatnia G, Choong YS. Theoretical investigation on structural, functional and epitope of a 12 kDa excretory-secretory protein from Toxoplasma gondii. BMC STRUCTURAL BIOLOGY 2012; 12:30. [PMID: 23181504 PMCID: PMC3542155 DOI: 10.1186/1472-6807-12-30] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 11/23/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND Toxoplasma gondii is an intracellular coccidian parasite that causes toxoplasmosis. It was estimated that more than one third of the world population is infected by T. gondii, and the disease is critical in fetuses and immunosuppressed patients. Thus, early detection is crucial for disease diagnosis and therapy. However, the current available toxoplasmosis diagnostic tests vary in their accuracy and the better ones are costly. RESULTS An earlier published work discovered a highly antigenic 12 kDa excretory-secretory (ES) protein of T. gondii which may potentially be used for the development of an antigen detection test for toxoplasmosis. However, the three-dimensional structure of the protein is unknown. Since epitope identification is important prior to designing of a specific antibody for an antigen-detection based diagnostic test, the structural elucidation of this protein is essential. In this study, we constructed a three dimensional model of the 12 kDa ES protein. The built structure possesses a thioredoxin backbone which consists of four α-helices flanking five β-strands at the center. Three potential epitopes (6-8 residues) which can be combined into one "single" epitope have been identified from the built structure as the most potential antibody binding site. CONCLUSION Together with specific antibody design, this work could contribute towards future development of an antigen detection test for toxoplasmosis.
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Affiliation(s)
- Yap Boon Wooi Tommy
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Rahmah Noordin
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Geita Saadatnia
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
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6
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Siloto RM, Weselake RJ. Site saturation mutagenesis: Methods and applications in protein engineering. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2012. [DOI: 10.1016/j.bcab.2012.03.010] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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7
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Hemmerlin A, Harwood JL, Bach TJ. A raison d'être for two distinct pathways in the early steps of plant isoprenoid biosynthesis? Prog Lipid Res 2011; 51:95-148. [PMID: 22197147 DOI: 10.1016/j.plipres.2011.12.001] [Citation(s) in RCA: 217] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/28/2011] [Accepted: 12/05/2011] [Indexed: 12/12/2022]
Abstract
When compared to other organisms, plants are atypical with respect to isoprenoid biosynthesis: they utilize two distinct and separately compartmentalized pathways to build up isoprene units. The co-existence of these pathways in the cytosol and in plastids might permit the synthesis of many vital compounds, being essential for a sessile organism. While substrate exchange across membranes has been shown for a variety of plant species, lack of complementation of strong phenotypes, resulting from inactivation of either the cytosolic pathway (growth and development defects) or the plastidial pathway (pigment bleaching), seems to be surprising at first sight. Hundreds of isoprenoids have been analyzed to determine their biosynthetic origins. It can be concluded that in angiosperms, under standard growth conditions, C₂₀-phytyl moieties, C₃₀-triterpenes and C₄₀-carotenoids are made nearly exclusively within compartmentalized pathways, while mixed origins are widespread for other types of isoprenoid-derived molecules. It seems likely that this coexistence is essential for the interaction of plants with their environment. A major purpose of this review is to summarize such observations, especially within an ecological and functional context and with some emphasis on regulation. This latter aspect still requires more work and present conclusions are preliminary, although some general features seem to exist.
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Affiliation(s)
- Andréa Hemmerlin
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, IBMP-CNRS-UPR2357, Université de Strasbourg, 28 Rue Goethe, F-67083 Strasbourg Cedex, France.
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8
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Conlan AR, Paddock ML, Axelrod HL, Cohen AE, Abresch EC, Wiley S, Roy M, Nechushtai R, Jennings PA. The novel 2Fe-2S outer mitochondrial protein mitoNEET displays conformational flexibility in its N-terminal cytoplasmic tethering domain. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:654-9. [PMID: 19574633 DOI: 10.1107/s1744309109019605] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 05/22/2009] [Indexed: 12/25/2022]
Abstract
A primary role for mitochondrial dysfunction is indicated in the pathogenesis of insulin resistance. A widely used drug for the treatment of type 2 diabetes is pioglitazone, a member of the thiazolidinedione class of molecules. MitoNEET, a 2Fe-2S outer mitochondrial membrane protein, binds pioglitazone [Colca et al. (2004), Am. J. Physiol. Endocrinol. Metab. 286, E252-E260]. The soluble domain of the human mitoNEET protein has been expressed C-terminal to the superfolder green fluorescent protein and the mitoNEET protein has been isolated. Comparison of the crystal structure of mitoNEET isolated from cleavage of the fusion protein (1.4 A resolution, R factor = 20.2%) with other solved structures shows that the CDGSH domains are superimposable, indicating proper assembly of mitoNEET. Furthermore, there is considerable flexibility in the position of the cytoplasmic tethering arms, resulting in two different conformations in the crystal structure. This flexibility affords multiple orientations on the outer mitochondrial membrane.
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Affiliation(s)
- Andrea R Conlan
- Department of Chemistry, University of California, San Diego, La Jolla, CA 92093, USA
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Pascual-García A, Abia D, Ortiz ÁR, Bastolla U. Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures. PLoS Comput Biol 2009; 5:e1000331. [PMID: 19325884 PMCID: PMC2654728 DOI: 10.1371/journal.pcbi.1000331] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Accepted: 02/11/2009] [Indexed: 11/19/2022] Open
Abstract
Structural classifications of proteins assume the existence of the fold, which is an intrinsic equivalence class of protein domains. Here, we test in which conditions such an equivalence class is compatible with objective similarity measures. We base our analysis on the transitive property of the equivalence relationship, requiring that similarity of A with B and B with C implies that A and C are also similar. Divergent gene evolution leads us to expect that the transitive property should approximately hold. However, if protein domains are a combination of recurrent short polypeptide fragments, as proposed by several authors, then similarity of partial fragments may violate the transitive property, favouring the continuous view of the protein structure space. We propose a measure to quantify the violations of the transitive property when a clustering algorithm joins elements into clusters, and we find out that such violations present a well defined and detectable cross-over point, from an approximately transitive regime at high structure similarity to a regime with large transitivity violations and large differences in length at low similarity. We argue that protein structure space is discrete and hierarchic classification is justified up to this cross-over point, whereas at lower similarities the structure space is continuous and it should be represented as a network. We have tested the qualitative behaviour of this measure, varying all the choices involved in the automatic classification procedure, i.e., domain decomposition, alignment algorithm, similarity score, and clustering algorithm, and we have found out that this behaviour is quite robust. The final classification depends on the chosen algorithms. We used the values of the clustering coefficient and the transitivity violations to select the optimal choices among those that we tested. Interestingly, this criterion also favours the agreement between automatic and expert classifications. As a domain set, we have selected a consensus set of 2,890 domains decomposed very similarly in SCOP and CATH. As an alignment algorithm, we used a global version of MAMMOTH developed in our group, which is both rapid and accurate. As a similarity measure, we used the size-normalized contact overlap, and as a clustering algorithm, we used average linkage. The resulting automatic classification at the cross-over point was more consistent than expert ones with respect to the structure similarity measure, with 86% of the clusters corresponding to subsets of either SCOP or CATH superfamilies and fewer than 5% containing domains in distinct folds according to both SCOP and CATH. Almost 15% of SCOP superfamilies and 10% of CATH superfamilies were split, consistent with the notion of fold change in protein evolution. These results were qualitatively robust for all choices that we tested, although we did not try to use alignment algorithms developed by other groups. Folds defined in SCOP and CATH would be completely joined in the regime of large transitivity violations where clustering is more arbitrary. Consistently, the agreement between SCOP and CATH at fold level was lower than their agreement with the automatic classification obtained using as a clustering algorithm, respectively, average linkage (for SCOP) or single linkage (for CATH). The networks representing significant evolutionary and structural relationships between clusters beyond the cross-over point may allow us to perform evolutionary, structural, or functional analyses beyond the limits of classification schemes. These networks and the underlying clusters are available at http://ub.cbm.uam.es/research/ProtNet.php Making order of the fast-growing information on proteins is essential for gaining evolutionary and functional knowledge. The most successful approaches to this task are based on classifications of protein structures, such as SCOP and CATH, which assume a discrete view of the protein structure space as a collection of separated equivalence classes (folds). However, several authors proposed that protein domains should be regarded as assemblies of polypeptide fragments, which implies that the protein–structure space is continuous. Here, we assess these views of domain space through the concept of transitivity; i.e., we test whether structure similarity of A with B and B with C implies that A and C are similar, as required for consistent classification. We find that the domain space is approximately transitive and discrete at high similarity and continuous at low similarity, where transitivity is severely violated. Comparing our classification at the cross-over similarity with CATH and SCOP, we find that they join proteins at low similarity where classification is inconsistent. Part of this discrepancy is due to structural divergence of homologous domains, which are forced to be in a single cluster in CATH and SCOP. Structural and evolutionary relationships between consistent clusters are represented as a network in our approach, going beyond current protein classification schemes. We conjecture that our results are related to a change of evolutionary regime, from uniparental divergent evolution for highly related domains to assembly of large fragments for which the classical tree representation is unsuitable.
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Affiliation(s)
| | - David Abia
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Ángel R. Ortiz
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Ugo Bastolla
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, Madrid, Spain
- * E-mail:
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10
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Cradle-loop barrels and the concept of metafolds in protein classification by natural descent. Curr Opin Struct Biol 2008; 18:358-65. [DOI: 10.1016/j.sbi.2008.02.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2007] [Accepted: 02/14/2008] [Indexed: 11/19/2022]
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11
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Piedra D, Lois S, de la Cruz X. Preservation of protein clefts in comparative models. BMC STRUCTURAL BIOLOGY 2008; 8:2. [PMID: 18199319 PMCID: PMC2249585 DOI: 10.1186/1472-6807-8-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Accepted: 01/16/2008] [Indexed: 11/29/2022]
Abstract
BACKGROUND Comparative, or homology, modelling of protein structures is the most widely used prediction method when the target protein has homologues of known structure. Given that the quality of a model may vary greatly, several studies have been devoted to identifying the factors that influence modelling results. These studies usually consider the protein as a whole, and only a few provide a separate discussion of the behaviour of biologically relevant features of the protein. Given the value of the latter for many applications, here we extended previous work by analysing the preservation of native protein clefts in homology models. We chose to examine clefts because of their role in protein function/structure, as they are usually the locus of protein-protein interactions, host the enzymes' active site, or, in the case of protein domains, can also be the locus of domain-domain interactions that lead to the structure of the whole protein. RESULTS We studied how the largest cleft of a protein varies in comparative models. To this end, we analysed a set of 53507 homology models that cover the whole sequence identity range, with a special emphasis on medium and low similarities. More precisely we examined how cleft quality - measured using six complementary parameters related to both global shape and local atomic environment, depends on the sequence identity between target and template proteins. In addition to this general analysis, we also explored the impact of a number of factors on cleft quality, and found that the relationship between quality and sequence identity varies depending on cleft rank amongst the set of protein clefts (when ordered according to size), and number of aligned residues. CONCLUSION We have examined cleft quality in homology models at a range of seq.id. levels. Our results provide a detailed view of how quality is affected by distinct parameters and thus may help the user of comparative modelling to determine the final quality and applicability of his/her cleft models. In addition, the large variability in model quality that we observed within each sequence bin, with good models present even at low sequence identities (between 20% and 30%), indicates that properly developed identification methods could be used to recover good cleft models in this sequence range.
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Affiliation(s)
- David Piedra
- Institut de Recerca Biomèdica, C/Josep Samitier, 1-5, 08028 Barcelona, Spain
| | - Sergi Lois
- Institut de Recerca Biomèdica, C/Josep Samitier, 1-5, 08028 Barcelona, Spain
- Instituto de Biología Molecular de Barcelona, CID, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Xavier de la Cruz
- Institut de Recerca Biomèdica, C/Josep Samitier, 1-5, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Hausrath AC, Goriely A. Continuous representations of proteins: construction of coordinate models from curvature profiles. J Struct Biol 2006; 158:267-81. [PMID: 17222563 DOI: 10.1016/j.jsb.2006.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2006] [Revised: 10/27/2006] [Accepted: 11/07/2006] [Indexed: 12/01/2022]
Abstract
A representation of proteins based on the geometry of space curves is described. This representation enables the application of continuum methods to the analysis of macromolecular structure and form that cannot be applied to the more familiar discrete atomic coordinate models. It is shown that the continuous modeling method defines the geometry of the protein fold very efficiently. An analytical solution for curve construction is employed from which both continuous and coordinate models can be obtained. The method is applied to five representative test proteins which are used to assess the accuracy and efficiency of the modeling procedure.
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Affiliation(s)
- A C Hausrath
- Department of Biochemistry and Molecular Biophysics, University of Arizona, 1041 E. Lowell, Tucson, AZ 85721, USA.
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13
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Yura K, Yamaguchi A, Go M. Coverage of whole proteome by structural genomics observed through protein homology modeling database. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2006; 7:65-76. [PMID: 17146617 PMCID: PMC1769342 DOI: 10.1007/s10969-006-9010-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Accepted: 08/08/2006] [Indexed: 11/07/2022]
Abstract
We have been developing FAMSBASE, a protein homology-modeling database of whole ORFs predicted from genome sequences. The latest update of FAMSBASE ( http://daisy.nagahama-i-bio.ac.jp/Famsbase/ ), which is based on the protein three-dimensional (3D) structures released by November 2003, contains modeled 3D structures for 368,724 open reading frames (ORFs) derived from genomes of 276 species, namely 17 archaebacterial, 130 eubacterial, 18 eukaryotic and 111 phage genomes. Those 276 genomes are predicted to have 734,193 ORFs in total and the current FAMSBASE contains protein 3D structure of approximately 50% of the ORF products. However, cases that a modeled 3D structure covers the whole part of an ORF product are rare. When portion of an ORF with 3D structure is compared in three kingdoms of life, in archaebacteria and eubacteria, approximately 60% of the ORFs have modeled 3D structures covering almost the entire amino acid sequences, however, the percentage falls to about 30% in eukaryotes. When annual differences in the number of ORFs with modeled 3D structure are calculated, the fraction of modeled 3D structures of soluble protein for archaebacteria is increased by 5%, and that for eubacteria by 7% in the last 3 years. Assuming that this rate would be maintained and that determination of 3D structures for predicted disordered regions is unattainable, whole soluble protein model structures of prokaryotes without the putative disordered regions will be in hand within 15 years. For eukaryotic proteins, they will be in hand within 25 years. The 3D structures we will have at those times are not the 3D structure of the entire proteins encoded in single ORFs, but the 3D structures of separate structural domains. Measuring or predicting spatial arrangements of structural domains in an ORF will then be a coming issue of structural genomics.
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Affiliation(s)
- Kei Yura
- Quantum Bioinformatics Team, Center for Computational Science and Engineering, Japan Atomic Energy Agency, Kyoto 619-0215, Japan.
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Zhang Y, Hubner IA, Arakaki AK, Shakhnovich E, Skolnick J. On the origin and highly likely completeness of single-domain protein structures. Proc Natl Acad Sci U S A 2006; 103:2605-10. [PMID: 16478803 PMCID: PMC1413790 DOI: 10.1073/pnas.0509379103] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The size and origin of the protein fold universe is of fundamental and practical importance. Analyzing randomly generated, compact sticky homopolypeptide conformations constructed in generic simplified and all-atom protein models, all have similar folds in the library of solved structures, the Protein Data Bank, and conversely, all compact, single-domain protein structures in the Protein Data Bank have structural analogues in the compact model set. Thus, both sets are highly likely complete, with the protein fold universe arising from compact conformations of hydrogen-bonded, secondary structures. Because side chains are represented by their Cbeta atoms, these results also suggest that the observed protein folds are insensitive to the details of side-chain packing. Sequence specificity enters both in fine-tuning the structure and thermodynamically stabilizing a given fold with respect to the set of alternatives. Scanning the models against a three-dimensional active-site library, close geometric matches are frequently found. Thus, the presence of active-site-like geometries also seems to be a consequence of the packing of compact, secondary structural elements. These results have significant implications for the evolution of protein structure and function.
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Affiliation(s)
- Yang Zhang
- *Center of Excellence in Bioinformatics, University at Buffalo, State University of New York, 901 Washington Street, Buffalo, NY 14203; and
| | - Isaac A. Hubner
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Adrian K. Arakaki
- *Center of Excellence in Bioinformatics, University at Buffalo, State University of New York, 901 Washington Street, Buffalo, NY 14203; and
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Jeffrey Skolnick
- *Center of Excellence in Bioinformatics, University at Buffalo, State University of New York, 901 Washington Street, Buffalo, NY 14203; and
- To whom correspondence should be sent at the present address:
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318. E-mail:
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Lee SJ, Lee DW, Choe EA, Hong YH, Kim SB, Kim BC, Pyun YR. Characterization of a thermoacidophilic L-arabinose isomerase from Alicyclobacillus acidocaldarius: role of Lys-269 in pH optimum. Appl Environ Microbiol 2006; 71:7888-96. [PMID: 16332764 PMCID: PMC1317409 DOI: 10.1128/aem.71.12.7888-7896.2005] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The araA gene encoding L-arabinose isomerase (AI) from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius was cloned, sequenced, and expressed in Escherichia coli. Analysis of the sequence revealed that the open reading frame of the araA gene consists of 1,491 bp that encodes a protein of 497 amino acid residues with a calculated molecular mass of 56,043 Da. Comparison of the deduced amino acid sequence of A. acidocaldarius AI (AAAI) with other AIs demonstrated that AAAI has 97% and 66% identities (99% and 83% similarities) to Geobacillus stearothermophilus AI (GSAI) and Bacillus halodurans AI (BHAI), respectively. The recombinant AAAI was purified to homogeneity by heat treatment, ion-exchange chromatography, and gel filtration. The purified enzyme showed maximal activity at pH 6.0 to 6.5 and 65 degrees C under the assay conditions used, and it required divalent cations such as Mn2+, Co2+, and Mg2+ for its activity. The isoelectric point (pI) of the enzyme was about 5.0 (calculated pI of 5.5). The apparent Km values of the recombinant AAAI for L-arabinose and D-galactose were 48.0 mM (Vmax, 35.5 U/mg) and 129 mM (Vmax, 7.5 U/mg), respectively, at pH 6 and 65 degrees C. Interestingly, although the biochemical properties of AAAI are quite similar to those of GSAI and BHAI, the three AIs from A. acidocaldarius (pH 6), G. stearothermophilus (pH 7), and B. halodurans (pH 8) exhibited different pH activity profiles. Based on alignment of the amino acid sequences of these homologous AIs, we propose that the Lys-269 residue of AAAI may be responsible for the ability of the enzyme to act at low pH. To verify the role of Lys-269, we prepared the mutants AAAI-K269E and BHAI-E268K by site-directed mutagenesis and compared their kinetic parameters with those of wild-type AIs at various pHs. The pH optima of both AAAI-K269E and BHAI-E268K were rendered by 1.0 units (pH 6 to 7 and 8 to 7, respectively) compared to the wild-type enzymes. In addition, the catalytic efficiency (kcat/Km) of each mutant at different pHs was significantly affected by an increase or decrease in Vmax. From these results, we propose that the position corresponding to the Lys-269 residue of AAAI could play an important role in the determination of the pH optima of homologous AIs.
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Affiliation(s)
- Sang-Jae Lee
- Department of Biotechnology, Yonsei University, Seodaemun-Gu, Shinchon-Dong 134, Seoul 120-749, Korea
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Noeske T, Gutcaits A, Parsons C, Weil T. Allosteric Modulation of Family 3 GPCRs. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/qsar.200510139] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Leulliot N, Quevillon-Cheruel S, Graille M, Schiltz M, Blondeau K, Janin J, Van Tilbeurgh H. Crystal structure of yeast YER010Cp, a knotable member of the RraA protein family. Protein Sci 2005; 14:2751-8. [PMID: 16195557 PMCID: PMC2253287 DOI: 10.1110/ps.051684005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We present here the structure of Yer010c protein of unknown function, solved by Multiple Anomalous Diffraction and revealing a common fold and oligomerization state with proteins of the regulator of ribonuclease activity A (RraA) family. In Escherichia coli, RraA has been shown to regulate the activity of ribonuclease E by direct interaction. The absence of ribonuclease E in yeast suggests a different function for this family member in this organism. Yer010cp has a few supplementary secondary structure elements and a deep pseudo-knot at the heart of the protein core. A tunnel at the interface between two monomers, lined with conserved charged residues, has unassigned residual electron density and may constitute an active site for a yet unknown activity.
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Affiliation(s)
- Nicolas Leulliot
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris-Sud, Bâtiment 430, 91405 Orsay, France.
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19
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Reinlib L. Meeting report: Structural determination of environmentally responsive proteins. ENVIRONMENTAL HEALTH PERSPECTIVES 2005; 113:1622-6. [PMID: 16263521 PMCID: PMC1310928 DOI: 10.1289/ehp.8129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The three-dimensional structure of gene products continues to be a missing lynchpin between linear genome sequences and our understanding of the normal and abnormal function of proteins and pathways. Enhanced activity in this area is likely to lead to better understanding of how discrete changes in molecular patterns and conformation underlie functional changes in protein complexes and, with it, sensitivity of an individual to an exposure. The National Institute of Environmental Health Sciences convened a workshop of experts in structural determination and environmental health to solicit advice for future research in structural resolution relative to environmentally responsive proteins and pathways. The highest priorities recommended by the workshop were to support studies of structure, analysis, control, and design of conformational and functional states at molecular resolution for environmentally responsive molecules and complexes; promote understanding of dynamics, kinetics, and ligand responses; investigate the mechanisms and steps in posttranslational modifications, protein partnering, impact of genetic polymorphisms on structure/function, and ligand interactions; and encourage integrated experimental and computational approaches. The workshop participants also saw value in improving the throughput and purity of protein samples and macromolecular assemblies; developing optimal processes for design, production, and assembly of macromolecular complexes; encouraging studies on protein-protein and macromolecular interactions; and examining assemblies of individual proteins and their functions in pathways of interest for environmental health.
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Affiliation(s)
- Leslie Reinlib
- Division of Extramural Research and Training, National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina 27709-2233, USA.
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20
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Abstract
CEP server () provides a web interface to the conformational epitope prediction algorithm developed in-house. The algorithm, apart from predicting conformational epitopes, also predicts antigenic determinants and sequential epitopes. The epitopes are predicted using 3D structure data of protein antigens, which can be visualized graphically. The algorithm employs structure-based Bioinformatics approach and solvent accessibility of amino acids in an explicit manner. Accuracy of the algorithm was found to be 75% when evaluated using X-ray crystal structures of Ag–Ab complexes available in the PDB. This is the first and the only method available for the prediction of conformational epitopes, which is an attempt to map probable antibody-binding sites of protein antigens.
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Affiliation(s)
- Urmila Kulkarni-Kale
- To whom correspondence should be addressed. Tel: +91 20 2569 0195/2569 2039; Fax: +91 20 2569 0087;
| | | | - A. S. Kolaskar
- Vice-Chancellor's office, University of PunePune 411 007, India
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21
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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: 1.5] [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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22
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Abstract
Dendritic cells (DCs) are a special type of leukocytes able to alert the immune system to the presence of infections. They play a central role in the initiation of both innate and adaptive immune responses. This particular DC feature is regulated by the activation of specific receptors at the cell surface called Toll-like receptors (TLRs) that bind a number of microbial products collectively referred to as microbial-associated molecular patterns (MAMP). TLRs initiate a cascade of events, which together define the process of DC maturation. This phenomenon allows DCs to progressively acquire varying specific functions. DC maturation depends on the nature of the perturbation and permits unique and efficient immune responses for each pathogen. In this review the discussion is focused on DCs in the context of interactions with pathogens and DC-specific functions are highlighted.
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Affiliation(s)
- Francesca Granucci
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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23
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Ceulemans H, Russell RB. Fast Fitting of Atomic Structures to Low-resolution Electron Density Maps by Surface Overlap Maximization. J Mol Biol 2004; 338:783-93. [PMID: 15099745 DOI: 10.1016/j.jmb.2004.02.066] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2003] [Revised: 02/18/2004] [Accepted: 02/19/2004] [Indexed: 11/21/2022]
Abstract
The complexities of X-ray crystallography and NMR spectroscopy for large protein complexes, and the comparative ease of approaches such as electron microscopy mean that low-resolution structures are often available long before their atomic resolution equivalents. To help bridge this gap in knowledge, we present 3SOM: an approach for finding the best fit of atomic resolution structures into lower-resolution density maps through surface overlap maximization. High-resolution templates (i.e. partial structures or models for multi-subunit complexes) and targets (lower-resolution maps) are initially represented as iso-surfaces. The latter are used first in a fast search for transformations that superimpose a significant portion of the target surface onto the template surface, which is quantified as surface overlap. The vast search space is reduced by considering key vectors that capture local surface information. The set of transformations with the highest surface overlap scores are then re-ranked by using more sophisticated scores including cross-correlation. We give a number of examples to illustrate the efficiency of the method and its restrictions. For targets for which partial complexes are available, the speed and performance of the method make it an attractive complement to existing methods, as many different hypotheses can be tested quickly on a single processor.
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Affiliation(s)
- Hugo Ceulemans
- EMBL Structural Bioinformatics Group, Meyerhofstrasse 1 D-69117 Heidelberg, Germany
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24
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Kim S, Zhang Z, Upchurch S, Isern N, Chen Y. Structure and DNA-binding Sites of the SWI1 AT-rich Interaction Domain (ARID) Suggest Determinants for Sequence-specific DNA Recognition. J Biol Chem 2004; 279:16670-6. [PMID: 14722072 DOI: 10.1074/jbc.m312115200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ARID (AT-rich interaction domain) is a homologous family of DNA-binding domains that occur in DNA-binding proteins from a wide variety of species, ranging from yeast to nematodes, insects, mammals, and plants. SWI1, a member of the SWI/SNF protein complex that is involved in chromatin remodeling during transcription, contains the ARID motif. The ARID domain of human SWI1 (also known as p270) does not select for a specific DNA sequence from a random sequence pool. The lack of sequence specificity shown by the SWI1 ARID domain stands in contrast to the other characterized ARID domains, which recognize specific AT-rich sequences. We have solved the three-dimensional structure of human SWI1 ARID using solution NMR methods. In addition, we have characterized nonspecific DNA binding by the SWI1 ARID domain. Results from this study indicate that a flexible, long, internal loop in the ARID motif is likely to be important for sequence-specific DNA recognition. The structure of the human SWI1 ARID domain also represents a distinct structural subfamily. Studies of ARID indicate that the boundary of DNA binding structural and functional domains can extend beyond the sequence homologous region in a homologous family of proteins. Structural studies of homologous domains such as the ARID family of DNA-binding domains should provide information to better predict the boundary of structural and functional domains in structural genomic studies.
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Affiliation(s)
- Suhkmann Kim
- Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
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25
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Abstract
Chalcone isomerase, an enzyme in the isoflavonoid pathway in plants, catalyzes the cyclization of chalcone into (2S)-naringenin. Chalcone isomerase sequence family and three-dimensional fold appeared to be unique to plants and has been proposed as a plant-specific gene marker. Using sensitive methods of sequence comparison and fold recognition, we have identified genes homologous to chalcone isomerase in all completely sequenced fungi, in slime molds, and in many gammaproteobacteria. The residues directly involved in the enzyme's catalytic function are among the best conserved across species, indicating that the newly discovered homologs are enzymatically active. At the same time, fungal and bacterial species that have chalcone isomerase-like genes tend to lack the orthologs of the upstream enzyme chalcone synthase, suggesting a novel variation of the pathway in these species.
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Affiliation(s)
- Michael Gensheimer
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA.
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26
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Miedlich SU, Gama L, Seuwen K, Wolf RM, Breitwieser GE. Homology modeling of the transmembrane domain of the human calcium sensing receptor and localization of an allosteric binding site. J Biol Chem 2003; 279:7254-63. [PMID: 14660633 DOI: 10.1074/jbc.m307191200] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A homology model for the human calcium sensing receptor (hCaR) transmembrane domain utilizing bovine rhodopsin (bRho) structural information was derived and tested by docking the allosteric antagonist, NPS 2143, followed by mutagenesis of predicted contact sites. Mutation of residues Phe-668 (helix II), Arg-680, or Phe-684 (helix III) to Ala (or Val or Leu) and Glu-837 (helix VII) to Ile (or Gln) reduced the inhibitory effects of NPS 2143 on [Ca2+]i responses. The calcimimetic NPS R-568 increases the potency of Ca2+ in functional assays of CaR. Mutations at Phe-668, Phe-684, or Glu-837 attenuated the effects of this compound, but mutations at Arg-680 had no effect. In all cases, mutant CaRs responded normally to Ca2+ or phenylalanine, which act at distinct site(s). Discrimination by the Arg-680 mutant is consistent with the structural differences between NPS 2143, which contains an alkyl bridge hydroxyl group, and NPS R-568, which does not. The homology model of the CaR transmembrane domain robustly accounts for binding of both an allosteric antagonist and agonist, which share a common site, and provides a basis for the development of more specific and/or potent allosteric modulators of CaR. These studies suggest that the bRho backbone can be used as a starting point for homology modeling of even distantly related G protein-coupled receptors and provide a rational framework for investigation of the contributions of the transmembrane domain to CaR function.
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Affiliation(s)
- Susanne U Miedlich
- Department of Biology, Syracuse University, Syracuse, New York 13244, USA
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27
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Aramini JM, Huang YJ, Cort JR, Goldsmith-Fischman S, Xiao R, Shih LY, Ho CK, Liu J, Rost B, Honig B, Kennedy MA, Acton TB, Montelione GT. Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Protein Sci 2003; 12:2823-30. [PMID: 14627742 PMCID: PMC2366990 DOI: 10.1110/ps.03359003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2003] [Revised: 08/08/2003] [Accepted: 08/18/2003] [Indexed: 10/26/2022]
Abstract
We report NMR assignments and solution structure of the 71-residue 30S ribosomal protein S28E from the archaean Pyrococcus horikoshii, target JR19 of the Northeast Structural Genomics Consortium. The structure, determined rapidly with the aid of automated backbone resonance assignment (AutoAssign) and automated structure determination (AutoStructure) software, is characterized by a four-stranded beta-sheet with a classic Greek-key topology and an oligonucleotide/oligosaccharide beta-barrel (OB) fold. The electrostatic surface of S28E exhibits positive and negative patches on opposite sides, the former constituting a putative binding site for RNA. The 13 C-terminal residues of the protein contain a consensus sequence motif constituting the signature of the S28E protein family. Surprisingly, this C-terminal segment is unstructured in solution.
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Affiliation(s)
- James M Aramini
- Northeast Structural Genomics Consortium Center for Advanced Biotechnology and Medicine (CABM), Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
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28
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Teller DC, Stenkamp RE, Palczewski K. Evolutionary analysis of rhodopsin and cone pigments: connecting the three-dimensional structure with spectral tuning and signal transfer. FEBS Lett 2003; 555:151-9. [PMID: 14630336 PMCID: PMC1468034 DOI: 10.1016/s0014-5793(03)01152-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Extensive sequence data and structural sampling of expressed proteins from different species lead to the idea that entire molecules or specific domain folds belong to large superfamilies of proteins. A subset of G protein-coupled receptors, one of the largest families involved in cellular signaling, rod and cone opsins are involved in phototransduction in photoreceptor cells. Here, the evolutionary analysis of opsin sequences and structures predicts key residues involved in the transmission of the signal from the binding site of the chromophore to the cytoplasmic surface and residues that are involved in the spectral tuning of opsins to short wavelengths of light.
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Affiliation(s)
- David C Teller
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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29
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Banatao DR, Altman RB, Klein TE. Microenvironment analysis and identification of magnesium binding sites in RNA. Nucleic Acids Res 2003; 31:4450-60. [PMID: 12888505 PMCID: PMC169872 DOI: 10.1093/nar/gkg471] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Interactions with magnesium (Mg2+) ions are essential for RNA folding and function. The locations and function of bound Mg2+ ions are difficult to characterize both experimentally and computationally. In particular, the P456 domain of the Tetrahymena thermophila group I intron, and a 58 nt 23s rRNA from Escherichia coli have been important systems for studying the role of Mg2+ binding in RNA, but characteristics of all the binding sites remain unclear. We therefore investigated the Mg2+ binding capabilities of these RNA systems using a computational approach to identify and further characterize their Mg2+ binding sites. The approach is based on the FEATURE algorithm, reported previously for microenvironment analysis of protein functional sites. We have determined novel physicochemical descriptions of site-bound and diffusely bound Mg2+ ions in RNA that are useful for prediction. Electrostatic calculations using the Non-Linear Poisson Boltzmann (NLPB) equation provided further evidence for the locations of site-bound ions. We confirmed the locations of experimentally determined sites and further differentiated between classes of ion binding. We also identified potentially important, high scoring sites in the group I intron that are not currently annotated as Mg2+ binding sites. We note their potential function and believe they deserve experimental follow-up.
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Affiliation(s)
- D Rey Banatao
- Department of Genetics and Stanford Medical Informatics, 251 Campus Drive, Stanford University, CA 94305, USA
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30
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Effken JA, Brewer BB, Patil A, Lamb GS, Verran JA, Carley KM. Using computational modeling to transform nursing data into actionable information. J Biomed Inform 2003; 36:351-61. [PMID: 14643731 DOI: 10.1016/j.jbi.2003.09.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Transforming organizational research data into actionable information nurses can use to improve patient outcomes remains a challenge. Available data are numerous, at multiple levels of analysis, and snapshots in time, which makes application difficult in a dynamically changing healthcare system. One potential solution is computational modeling. We describe our use of OrgAhead, a theoretically based computational modeling program developed at Carnegie Mellon University, to transform data into actionable nursing information. We calibrated the model by using data from 16 actual patient care units to adjust model parameters until performance of simulated units ordered in the same way as observed performance of the actual units 80% of the time. In future research, we will use OrgAhead to generate hypotheses about changes nurses might make to improve patient outcomes, help nurses use these hypotheses to identify and implement changes on their units, and then measure the impact of those changes on patient outcomes.
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Affiliation(s)
- Judith A Effken
- College of Nursing, University of Arizona, Tucson, AZ 85721-0203, USA.
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31
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Ouzounis CA, Coulson RMR, Enright AJ, Kunin V, Pereira-Leal JB. Classification schemes for protein structure and function. Nat Rev Genet 2003; 4:508-19. [PMID: 12838343 DOI: 10.1038/nrg1113] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We examine the structural and functional classifications of the protein universe, providing an overview of the existing classification schemes, their features and inter-relationships. We argue that a unified scheme should be based on a natural classification approach and that more comparative analyses of the present schemes are required both to understand their limitations and to help delimit the number of known protein folds and their corresponding functional roles in cells.
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Affiliation(s)
- Christos A Ouzounis
- Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.
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32
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Liang MP, Banatao DR, Klein TE, Brutlag DL, Altman RB. WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures. Nucleic Acids Res 2003; 31:3324-7. [PMID: 12824318 PMCID: PMC168960 DOI: 10.1093/nar/gkg553] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
WebFEATURE (http://feature.stanford.edu/webfeature/) is a web-accessible structural analysis tool that allows users to scan query structures for functional sites in both proteins and nucleic acids. WebFEATURE is the public interface to the scanning algorithm of the FEATURE package, a supervised learning algorithm for creating and identifying 3D, physicochemical motifs in molecular structures. Given an input structure or Protein Data Bank identifier (PDB ID), and a statistical model of a functional site, WebFEATURE will return rank-scored 'hits' in 3D space that identify regions in the structure where similar distributions of physicochemical properties occur relative to the site model. Users can visualize and interactively manipulate scored hits and the query structure in web browsers that support the Chime plug-in. Alternatively, results can be downloaded and visualized through other freely available molecular modeling tools, like RasMol, PyMOL and Chimera. A major application of WebFEATURE is in rapid annotation of function to structures in the context of structural genomics.
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Affiliation(s)
- Mike P Liang
- Department of Genetics and Stanford Medical Informatics, 251 Campus Drive, Stanford University, Stanford, CA 94305, USA
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33
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Abstract
Groups of related genes abound in large eukaryotic genomes. In such 'subgenomes', homology modeling carried out for a few genes will probably have relevance to the entire group. Subgenomes also afford unique ways of determining protein structural information. In addition to analyses based on the quantification of residue variability in paralogs, two-way comparisons, both within and among species, help to disclose functional amino acids. Comparative studies of gene families throughout the mammalian genome will also help elucidate the functional significance of single nucleotide polymorphisms in coding regions.
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Affiliation(s)
- Orna Man
- The Crown Human Genome Center, The Weizmann Institute of Science, Rehovot, 76100, Israel
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34
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Pineda-Lucena A, Liao JCC, Cort JR, Yee A, Kennedy MA, Edwards AM, Arrowsmith CH. A novel member of the split betaalphabeta fold: Solution structure of the hypothetical protein YML108W from Saccharomyces cerevisiae. Protein Sci 2003; 12:1136-40. [PMID: 12717036 PMCID: PMC2323884 DOI: 10.1110/ps.0240903] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2002] [Revised: 01/28/2003] [Accepted: 02/06/2003] [Indexed: 10/27/2022]
Abstract
As part of the Northeast Structural Genomics Consortium pilot project focused on small eukaryotic proteins and protein domains, we have determined the NMR structure of the protein encoded by ORF YML108W from Saccharomyces cerevisiae. YML108W belongs to one of the numerous structural proteomics targets whose biological function is unknown. Moreover, this protein does not have sequence similarity to any other protein. The NMR structure of YML108W consists of a four-stranded beta-sheet with strand order 2143 and two alpha-helices, with an overall topology of betabetaalphabetabetaalpha. Strand beta1 runs parallel to beta4, and beta2:beta1 and beta4:beta3 pairs are arranged in an antiparallel fashion. Although this fold belongs to the split betaalphabeta family, it appears to be unique among this family; it is a novel arrangement of secondary structure, thereby expanding the universe of protein folds.
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Affiliation(s)
- Antonio Pineda-Lucena
- Division of Molecular and Structural Biology, Ontario Cancer Institute and University of Toronto, Toronto, Ontario M5G 2M9, Canada
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35
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Hosfield D, Palan J, Hilgers M, Scheibe D, McRee DE, Stevens RC. A fully integrated protein crystallization platform for small-molecule drug discovery. J Struct Biol 2003; 142:207-17. [PMID: 12718932 DOI: 10.1016/s1047-8477(03)00051-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure-based drug discovery in the pharmaceutical industry benefits from cost-efficient methodologies that quickly assess the feasibility of specific, often refractory, protein targets to form well-diffracting crystals. By tightly coupling construct and purification diversity with nanovolume crystallization, the Structural Biology Group at Syrrx has developed such a platform to support its small-molecule drug-discovery program. During the past 18 months of operation at Syrrx, the Structural Biology Group has executed several million crystallization and imaging trials on over 400 unique drug-discovery targets. Here, key components of the platform, as well as an analysis of some experimental results that allowed for platform optimization, will be described.
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Affiliation(s)
- David Hosfield
- Syrrx, Inc., 10410 Science Center Drive, San Diego, CA 92121, USA
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36
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Lan N, Montelione GT, Gerstein M. Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level. Curr Opin Chem Biol 2003; 7:44-54. [PMID: 12547426 DOI: 10.1016/s1367-5931(02)00020-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A principal aim of post-genomic biology is elucidating the structures, functions and biochemical properties of all gene products in a genome. However, to adequately comprehend such a large amount of information we need new descriptions of proteins that scale to the genomic level. In short, we need a unified ontology for proteomics. Much progress has been made towards this end, including a variety of approaches to systematic structural and functional classification and initial work towards developing standardized, unified descriptions for protein properties. In relation to function, there is a particularly great diversity of approaches, involving placing a protein in structured hierarchies or more-generalized networks and a recent approach based on circumscribing a protein's function through systematic enumeration of molecular interactions.
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Affiliation(s)
- Ning Lan
- Department of Molecular Biophysics, New Haven, CT 06520, USA.
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37
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Abstract
The unprecedented increase in the number of new protein sequences arising from genomics and proteomics highlights directly the need for methods to rapidly and reliably determine the molecular and cellular functions of these proteins. One such approach, structural genomics, aims to delineate the total repertoire of protein folds, thereby providing three-dimensional portraits for all proteins in a living organism and to infer molecular functions of the proteins. The goal of obtaining protein structures on a genomic scale has motivated the development of high-throughput technologies for macromolecular structure determination, which have begun to produce structures at a greater rate than previously possible. These new structures have revealed many unexpected functional and evolution relationships that were hidden at the sequence level.
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Affiliation(s)
- Chao Zhang
- Department of Chemistry, Lawrence Berkeley National Laboratory, University of California at Berkeley, Berkeley, CA 94720, USA
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