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Bellucci M, Pompa A, De Marcos Lousa C, Panfili E, Orecchini E, Maricchiolo E, Fraternale D, Orabona C, De Marchis F, Pallotta MT. Human Indoleamine 2,3-dioxygenase 1 (IDO1) Expressed in Plant Cells Induces Kynurenine Production. Int J Mol Sci 2021; 22:5102. [PMID: 34065885 PMCID: PMC8151846 DOI: 10.3390/ijms22105102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/21/2021] [Accepted: 05/08/2021] [Indexed: 01/07/2023] Open
Abstract
Genetic engineering of plants has turned out to be an attractive approach to produce various secondary metabolites. Here, we attempted to produce kynurenine, a health-promoting metabolite, in plants of Nicotiana tabacum (tobacco) transformed by Agrobacterium tumefaciens with the gene, coding for human indoleamine 2,3-dioxygenase 1 (IDO1), an enzyme responsible for the kynurenine production because of tryptophan degradation. The presence of IDO1 gene in transgenic plants was confirmed by PCR, but the protein failed to be detected. To confer higher stability to the heterologous human IDO1 protein and to provide a more sensitive method to detect the protein of interest, we cloned a gene construct coding for IDO1-GFP. Analysis of transiently transfected tobacco protoplasts demonstrated that the IDO1-GFP gene led to the expression of a detectable protein and to the production of kynurenine in the protoplast medium. Interestingly, the intracellular localisation of human IDO1 in plant cells is similar to that found in mammal cells, mainly in cytosol, but in early endosomes as well. To the best of our knowledge, this is the first report on the expression of human IDO1 enzyme capable of secreting kynurenines in plant cells.
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Affiliation(s)
- Michele Bellucci
- Institute of Biosciences and Bioresources, National Research Council of Italy, 06128 Perugia, Italy; (M.B.); (A.P.)
| | - Andrea Pompa
- Institute of Biosciences and Bioresources, National Research Council of Italy, 06128 Perugia, Italy; (M.B.); (A.P.)
- Department of Biomolecular Sciences, University Carlo Bo, 61029 Urbino, Italy; (E.M.); (D.F.)
| | - Carine De Marcos Lousa
- Centre for Biomedical Sciences, School of Clinical and Applied Sciences, Leeds Beckett University, Leeds LS13HE, UK;
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS29JT, UK
| | - Eleonora Panfili
- Department of Medicine and Surgery, University of Perugia, 06128 Perugia, Italy; (E.P.); (E.O.); (C.O.)
| | - Elena Orecchini
- Department of Medicine and Surgery, University of Perugia, 06128 Perugia, Italy; (E.P.); (E.O.); (C.O.)
| | - Elisa Maricchiolo
- Department of Biomolecular Sciences, University Carlo Bo, 61029 Urbino, Italy; (E.M.); (D.F.)
| | - Daniele Fraternale
- Department of Biomolecular Sciences, University Carlo Bo, 61029 Urbino, Italy; (E.M.); (D.F.)
| | - Ciriana Orabona
- Department of Medicine and Surgery, University of Perugia, 06128 Perugia, Italy; (E.P.); (E.O.); (C.O.)
| | - Francesca De Marchis
- Institute of Biosciences and Bioresources, National Research Council of Italy, 06128 Perugia, Italy; (M.B.); (A.P.)
| | - Maria Teresa Pallotta
- Department of Medicine and Surgery, University of Perugia, 06128 Perugia, Italy; (E.P.); (E.O.); (C.O.)
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Duffy binding-like 1α adhesin from Plasmodium falciparum recognizes ABH histo-blood group saccharide in a type specific manner. Carbohydr Polym 2019; 207:266-275. [PMID: 30600009 DOI: 10.1016/j.carbpol.2018.11.082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/30/2018] [Accepted: 11/25/2018] [Indexed: 11/20/2022]
Abstract
The ability of erythrocytes, infected by Plasmodium falciparum, to adhere to endothelial cells (cytoadherence) and to capture uninfected erythrocyte (rosetting) is the leading cause of death by severe malaria. Evidences link the binding of the adhesin Duffy Binding Like1-α (DBL1α) domain to the ABH histo-blood antigens with formation of rosettes. Inspired by this very close relationship between the disease susceptibility and individual blood type, here we investigate the structural requirements involved in the interaction of DBL1α with A, B and H histo-blood determinants and their subtypes. Our results evidence the high preference of DBL1α to A epitopes, in comparison to B and H epitopes. DBL1α interacts with ABH epitopes in subtype specific manner, presenting a remarkable affinity for type 2 structures, Fucα1-2Galβ1-4GlcNAcβ1, particularly the A2 epitope. The contacts made by DBL1α binding pocket and the ABH histo-blood groups were mapped by theoretical methods and supported by NMR experiments.
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Naderi M, Govindaraj RG, Brylinski M. eModel-BDB: a database of comparative structure models of drug-target interactions from the Binding Database. Gigascience 2018; 7:5057873. [PMID: 30052959 PMCID: PMC6131211 DOI: 10.1093/gigascience/giy091] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 07/16/2018] [Indexed: 01/14/2023] Open
Abstract
Background The structural information on proteins in their ligand-bound conformational state is invaluable for protein function studies and rational drug design. Compared to the number of available sequences, not only is the repertoire of the experimentally determined structures of holo-proteins limited, these structures do not always include pharmacologically relevant compounds at their binding sites. In addition, binding affinity databases provide vast quantities of information on interactions between drug-like molecules and their targets, however, often lacking structural data. On that account, there is a need for computational methods to complement existing repositories by constructing the atomic-level models of drug-protein assemblies that will not be determined experimentally in the near future. Results We created eModel-BDB, a database of 200,005 comparative models of drug-bound proteins based on 1,391,403 interaction data obtained from the Binding Database and the PDB library of 31 January 2017. Complex models in eModel-BDB were generated with a collection of the state-of-the-art techniques, including protein meta-threading, template-based structure modeling, refinement and binding site detection, and ligand similarity-based docking. In addition to a rigorous quality control maintained during dataset generation, a subset of weakly homologous models was selected for the retrospective validation against experimental structural data recently deposited to the Protein Data Bank. Validation results indicate that eModel-BDB contains models that are accurate not only at the global protein structure level but also with respect to the atomic details of bound ligands. Conclusions Freely available eModel-BDB can be used to support structure-based drug discovery and repositioning, drug target identification, and protein structure determination.
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Affiliation(s)
- Misagh Naderi
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg, Baton Rouge, LA 70803, USA
| | - Rajiv Gandhi Govindaraj
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg, Baton Rouge, LA 70803, USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg, Baton Rouge, LA 70803, USA.,Center for Computation & Technology, Louisiana State University, 2054 Digital Media Center, Baton Rouge, LA 70803, USA
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4
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Wiebke-Strohm B, Ligabue-Braun R, Rechenmacher C, De Oliveira-Busatto LA, Carlini CR, Bodanese-Zanettini MH. Structural and transcriptional characterization of a novel member of the soybean urease gene family. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 101:96-104. [PMID: 26874294 DOI: 10.1016/j.plaphy.2016.01.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 01/28/2016] [Accepted: 01/28/2016] [Indexed: 06/05/2023]
Abstract
In plants, ureases have been related to urea degradation, to defense against pathogenic fungi and phytophagous insects, and to the soybean-Bradyrhizobium japonicum symbiosis. Two urease isoforms have been described for soybean: the embryo-specific, encoded by Eu1 gene, and the ubiquitous urease, encoded by Eu4. A third urease-encoding locus exists in the completed soybean genome. The gene was designated Eu5 and the putative product of its ORF as SBU-III. Phylogenetic analysis shows that 41 plant, moss and algal ureases have diverged from a common ancestor protein, but ureases from monocots, eudicots and ancient species have evolved independently. Genomes of ancient organisms present a single urease-encoding gene and urease-encoding gene duplication has occurred independently along the evolution of some eudicot species. SBU-III has a shorter amino acid sequence, since many gaps are found when compared to other sequences. A mutation in a highly conserved amino acid residue suggests absence of ureolytic activity, but the overall protein architecture remains very similar to the other ureases. The expression profile of urease-encoding genes in different organs and developmental stages was determined by RT-qPCR. Eu5 transcripts were detected in seeds one day after dormancy break, roots of young plants and embryos of developing seeds. Eu1 and Eu4 transcripts were found in all analyzed organs, but Eu4 expression was more prominent in seeds one day after dormancy break whereas Eu1 predominated in developing seeds. The evidence suggests that SBU-III may not be involved in nitrogen availability to plants, but it could be involved in other biological role(s).
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Affiliation(s)
- Beatriz Wiebke-Strohm
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil.
| | - Rodrigo Ligabue-Braun
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, 91501-970, Porto Alegre, RS, Brazil.
| | - Ciliana Rechenmacher
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil.
| | - Luisa Abruzzi De Oliveira-Busatto
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil.
| | - Célia Regina Carlini
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, 91501-970, Porto Alegre, RS, Brazil; Instituto do Cérebro, Pontifícia Universidade do Rio Grande do Sul (PUCRS), Av. Ipiranga 6690, 90610-000, Porto Alegre, Brazil.
| | - Maria Helena Bodanese-Zanettini
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil.
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Abstract
Structural proteomics aims to understand the structural basis of protein interactions and functions. A prerequisite for this is the availability of 3D protein structures that mediate the biochemical interactions. The explosion in the number of available gene sequences set the stage for the next step in genome-scale projects -- to obtain 3D structures for each protein. To achieve this ambitious goal, the slow and costly structure determination experiments are supplemented with theoretical approaches. The current state and recent advances in structure modeling approaches are reviewed here, with special emphasis on comparative protein structure modeling techniques.
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Affiliation(s)
- András Fiser
- Department of Biochemistry, Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA.
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6
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Pol-Fachin L, Verli H. Structural glycobiology of heparin dynamics on the exosite 2 of coagulation cascade proteases: Implications for glycosaminoglycans antithrombotic activity. Glycobiology 2013; 24:97-105. [PMID: 24201825 DOI: 10.1093/glycob/cwt095] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
fIIa and fXa are two of the main targets of antithrombin, a serine proteases inhibitor that plays a major role in the regulation of blood clotting. The formation of ternary complexes between such molecules and glycosaminoglycans, as heparin, is the main path for inhibiting those enzymes, which may occur through two distinct mechanisms of action. While these serine proteases present distinct susceptibilities to these paths, in which fIIa demands an interaction with heparin, neither the molecular basis of this differential inhibition nor the role of fIIa glycosylation on this process is fully understood. Thus, the present work evaluated through molecular dynamics simulations the effects of glycosylation on fIIa and the consequences of heparin binding to both proteases function and dynamics. Based on the obtained data, fIIa N-linked glycan promoted an increase in the active site pocket size by stabilizing regions that encircle it, while heparin binding was observed to reverse such an effect. Additionally, heparin orientation observed on the surface of fIIa, but not fXa, allows a linear long-chain heparin binding to antithrombin in ternary complexes. Finally, the enzymes catalytic triad organization was disrupted due to a strong glycosaminoglycan binding to the proteases exosite 2. Such data support an atomic-level explanation for the higher inhibition constant of the antithrombin-heparin complex over fIIa than fXa, as well as for the different susceptibilities of those enzymes for antithrombin mechanisms of action.
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Affiliation(s)
- Laercio Pol-Fachin
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil
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7
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Mulinari F, Becker-Ritt AB, Demartini DR, Ligabue-Braun R, Stanisçuaski F, Verli H, Fragoso RR, Schroeder EK, Carlini CR, Grossi-de-Sá MF. Characterization of JBURE-IIb isoform of Canavalia ensiformis (L.) DC urease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1758-68. [PMID: 21893219 DOI: 10.1016/j.bbapap.2011.07.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 07/20/2011] [Accepted: 07/22/2011] [Indexed: 11/29/2022]
Abstract
Ureases, nickel-dependent enzymes that catalyze the hydrolysis of urea into ammonia and bicarbonate, are widespread in plants, bacteria, and fungi. Previously, we cloned a cDNA encoding a Canavalia ensiformis urease isoform named JBURE-II, corresponding to a putative smaller urease protein (78kDa) when compared to other plant ureases. Aiming to produce the recombinant protein, we obtained jbure-IIb, with different 3' and 5' ends, encoding a 90kDa urease. Three peptides unique to the JBURE-II/-IIb protein were detected by mass spectrometry in seed extracts, indicating that jbure-II/-IIb is a functional gene. Comparative modeling indicates that JBURE-IIb urease has an overall shape almost identical to C. ensiformis major urease JBURE-I with all residues critical for urease activity. The cDNA was cloned into the pET101 vector and the recombinant protein was produced in Escherichia coli. The JBURE-IIb protein, although enzymatically inactive presumably due to the absence of Ni atoms in its active site, impaired the growth of a phytopathogenic fungus and showed entomotoxic properties, inhibiting diuresis of Rhodnius prolixus isolated Malpighian tubules, in concentrations similar to those reported for JBURE-I and canatoxin. The antifungal and entomotoxic properties of the recombinant JBURE-IIb apourease are consistent with a protective role of ureases in plants.
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Affiliation(s)
- Fernanda Mulinari
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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Venkateswaran JG, Song B, Kahveci T, Jermaine C. TRIAL: a tool for finding distant structural similarities. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011; 8:819-831. [PMID: 21393655 DOI: 10.1109/tcbb.2009.28] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Finding structural similarities in distantly related proteins can reveal functional relationships that can not be identified using sequence comparison. Given two proteins A and B and threshold ε Å, we develop an algorithm, TRiplet-based Iterative ALignment (TRIAL) for computing the transformation of B that maximizes the number of aligned residues such that the root mean square deviation (RMSD) of the alignment is at most ε Å. Our algorithm is designed with the specific goal of effectively handling proteins with low similarity in primary structure, where existing algorithms perform particularly poorly. Experiments show that our method outperforms existing methods. TRIAL alignment brings the secondary structures of distantly related proteins to similar orientations. It also finds larger number of secondary structure matches at lower RMSD values and increased overall alignment lengths. Its classification accuracy is up to 63 percent better than other methods, including CE and DALI. TRIAL successfully aligns 83 percent of the residues from the smaller protein in reasonable time while other methods align only 29 to 65 percent of the residues for the same set of proteins.
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Okazaki M, Higuchi K, Aouini A, Ezura H. Lowering intercellular melatonin levels by transgenic analysis of indoleamine 2,3-dioxygenase from rice in tomato plants. J Pineal Res 2010; 49:239-47. [PMID: 20609074 DOI: 10.1111/j.1600-079x.2010.00788.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Melatonin exists in numerous living organisms including vertebrates, insects, fungi, bacteria, and plants. Extensive studies have been conducted on the physiological roles of melatonin in various plant species. In plants, melatonin seems to act in antioxidant protection, as a growth promoter, and in photoperiodism. However, the mechanisms by which melatonin carries out these roles remain unclear. We manipulated the endogenous melatonin content in tomato plants by modifying the metabolic enzyme indoleamine 2,3-dioxygenase (IDO). The OsIDO gene was isolated from rice (Oryza sativa) and characterized using 3-D homology modeling and reverse genetic approaches. The amino acid sequence of OsIDO showed high homology to the Ustilago maydis IDO. The 3-D model structure of OsIDO is composed of a small and a large domain. Transgenic tomato plants constitutively expressing the OsIDO gene exhibited a decrease in their melatonin content. Moreover, the number of lateral leaflets decreased in transgenic plants. Protein extracts taken from these plants showed activity degradation, demonstrating the function of OsIDO. These results suggest the involvement of IDO in plant melatonin metabolism and a possible role in plant leaf development.
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MESH Headings
- Amino Acid Sequence
- Indoleamine-Pyrrole 2,3,-Dioxygenase/chemistry
- Indoleamine-Pyrrole 2,3,-Dioxygenase/classification
- Indoleamine-Pyrrole 2,3,-Dioxygenase/genetics
- Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism
- Solanum lycopersicum/genetics
- Solanum lycopersicum/metabolism
- Melatonin/genetics
- Melatonin/metabolism
- Molecular Sequence Data
- Oryza/enzymology
- Oryza/genetics
- Phylogeny
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Sequence Homology, Amino Acid
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Affiliation(s)
- Masateru Okazaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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10
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Campanaro S, Treu L, Valle G. Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates. BMC Evol Biol 2008; 8:313. [PMID: 19014525 PMCID: PMC2600651 DOI: 10.1186/1471-2148-8-313] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2008] [Accepted: 11/13/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Abyssal microorganisms have evolved particular features that enable them to grow in their extreme habitat. Genes belonging to specific functional categories are known to be particularly susceptible to high-pressure; therefore, they should show some evidence of positive selection. To verify this hypothesis we computed the amino acid substitution rates between two deep-sea microorganisms, Photobacterium profundum SS9 and Shewanella benthica KT99, and their respective shallow water relatives. RESULTS A statistical analysis of all the orthologs, led to the identification of positive selected (PS) genes, which were then used to evaluate adaptation strategies. We were able to establish "Motility" and "Transport" as two classes significantly enriched with PS genes. The prevalence of transporters led us to analyze variable amino acids (PS sites) by mapping them according to their membrane topology, the results showed a higher frequency of substitutions in the extra-cellular compartment. A similar analysis was performed on soluble proteins, mapping the PS sites on the 3D structure, revealing a prevalence of substitutions on the protein surface. Finally, the presence of some flagellar proteins in the Vibrionaceae PS list confirms the importance of bacterial motility as a SS9 specific adaptation strategy. CONCLUSION The approach presented in this paper is suitable for identifying molecular adaptations to particular environmental conditions. The statistical method takes into account differences in the ratio between non-synonymous to synonymous substitutions, thus allowing the detection of the genes that underwent positive selection. We found that positive selection in deep-sea adapted bacteria targets a wide range of functions, for example solute transport, protein translocation, DNA synthesis and motility. From these data clearly emerges an involvement of the transport and metabolism processes in the deep-sea adaptation strategy of both bathytypes considered, whereas the adaptation of other biological processes seems to be specific to either one or the other. An important role is hypothesized for five PS genes belonging to the transport category that had been previously identified as differentially expressed in microarray experiments. Strikingly, structural mapping of PS sites performed independently on membrane and soluble proteins revealed that residues under positive selection tend to occur in specific protein regions.
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Affiliation(s)
- Stefano Campanaro
- CRIBI Biotechnology Centre, Department of Biology, University of Padua, Via U. Bassi 38/b, 35121, Padua, Italy.
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Parthiban M, Shanmughavel P. Three dimensional modeling of N-terminal region of galanin and its interaction with the galanin receptor. Bioinformation 2007; 2:119-25. [PMID: 18288336 PMCID: PMC2248450 DOI: 10.6026/97320630002119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Accepted: 11/09/2007] [Indexed: 02/02/2023] Open
Abstract
The neuropeptide galanin comes under the powerful and versatile modulators of classical neurotransmitters and is present in brain tissues, which are intimately involved in epileptogenesis. It acts as appealing targets for studying basic mechanisms of seizure initiation and arrest, and for the development of novel approaches for various neurodegenerative diseases. Galanin is widely distributed in the mammalian brain which controls various processes such as sensation of pain, learning, feeding, sexual behaviour, carcinogenesis, pathophysiology of neuroendocrine tumors and others. The function of galanin can be exploited through its interaction with three G-protein coupled receptors subtypes such as GalR1, GalR2 and GalR3. The N-terminal region of galanin comprises about highly conserved 15 amino acid residues, which act as the crucial region for agonist-receptor binding. We have constructed a theoretical structural model for the N-terminal region of galanin from Homo sapiens by homology modeling. The stereochemistry of the model was checked using PROCHECK. The functionally conserved regions were identified by surface mapping of phylogenetic information generated by online web algorithm ConSurf. The docking studies on the pharmacologically important galanin receptors with the theoretical model of N-terminal region of galanin predicted crucial residues for binding which would be useful in the development of novel leads for neurodegenerative disorders.
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Affiliation(s)
- Marimuthu Parthiban
- Department of Bioinformatics, Bharathiar University, Coimbatore - 641046, India
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12
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Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH, Dunbrack RL, Fidelis K, Frank J, Godzik A, Henrick K, Joachimiak A, Heymann B, Jones D, Markley JL, Moult J, Montelione GT, Orengo C, Rossmann MG, Rost B, Saibil H, Schwede T, Standley DM, Westbrook JD. Outcome of a workshop on archiving structural models of biological macromolecules. Structure 2006; 14:1211-7. [PMID: 16955948 DOI: 10.1016/j.str.2006.06.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Helen M Berman
- The Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
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13
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Bellsolell L, Cho-Park PF, Poulin F, Sonenberg N, Burley SK. Two structurally atypical HEAT domains in the C-terminal portion of human eIF4G support binding to eIF4A and Mnk1. Structure 2006; 14:913-23. [PMID: 16698552 DOI: 10.1016/j.str.2006.03.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Revised: 03/20/2006] [Accepted: 03/21/2006] [Indexed: 10/24/2022]
Abstract
The X-ray structure of the C-terminal region of human eukaryotic translation initiation factor 4G (eIF4G) has been determined at 2.2 A resolution, revealing two atypical HEAT-repeat domains. eIF4G recruits various translation factors and the 40S ribosomal subunit to the mRNA 5' end. In higher eukaryotes, the C terminus of eIF4G (4G/C) supports translational regulation by recruiting eIF4A, an RNA helicase, and Mnk1, the kinase responsible for phosphorylating eIF4E. Structure-guided surface mutagenesis and protein-protein interaction assays were used to identify binding sites for eIF4A and Mnk1 within the HEAT-repeats of 4G/C. p97/DAP5, a translational modulator homologous to eIF4G, lacks an eIF4A binding site in the corresponding region. The second atypical HEAT domain of the 4G/C binds Mnk1 using two conserved aromatic/acidic-box (AA-box) motifs. Within the first AA-box, the aromatic residues contribute to the hydrophobic core of the domain, while the acidic residues form a negatively charged surface feature suitable for electrostatic interactions with basic residues in Mnk1.
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Affiliation(s)
- Lluís Bellsolell
- Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York 10021, USA
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14
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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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15
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Camoglu O, Kahveci T, Singh AK. Index-based similarity search for protein structure databases. J Bioinform Comput Biol 2004; 2:99-126. [PMID: 15272435 DOI: 10.1142/s0219720004000491] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2003] [Revised: 11/21/2003] [Accepted: 12/07/2003] [Indexed: 11/18/2022]
Abstract
We propose new methods for finding similarities in protein structure databases. These methods extract feature vectors on triplets of SSEs (Secondary Structure Elements) of proteins. The feature vectors are then indexed using a multidimensional index structure. Our first technique considers the problem of finding proteins similar to a given query protein in a protein dataset. It quickly finds promising proteins using the index structure. These proteins are then aligned to the query protein using a popular pairwise alignment tool such as VAST. We also develop a novel statistical model to estimate the goodness of a match using the SSEs. Our second technique considers the problem of joining two protein datasets to find an all-to-all similarity. Experimental results show that our techniques improve the pruning time of VAST 3 to 3.5 times, while keeping the sensitivity similar. Our technique can also be incorporated with DALI and CE to improve their running times by a factor of 2 and 2.7 respectively. The software is available online at http://bioserver.cs.ucsb.edu/.
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Affiliation(s)
- Orhan Camoglu
- Department of Computer Science, University of California, Santa Barbara, CA 93106, USA.
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16
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Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 2004; 32:D217-22. [PMID: 14681398 PMCID: PMC308829 DOI: 10.1093/nar/gkh095] [Citation(s) in RCA: 220] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on the MODELLER package for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE uses the MySQL relational database management system for flexible querying and CHIMERA for viewing the sequences and structures (http://www.cgl.ucsf.edu/chimera/). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different data sets. The largest data set contains 1,26,629 models for domains in 659,495 out of 1,182,126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only models based on alignments with significant similarity scores and models assessed to have the correct fold despite insignificant alignments are included. Another model data set supports target selection and structure-based annotation by the New York Structural Genomics Research Consortium; e.g. the 53 new structures produced by the consortium allowed us to characterize structurally 24,113 sequences. MODBASE also contains binding site predictions for small ligands and a set of predicted interactions between pairs of modeled sequences from the same genome. Our other resources associated with MODBASE include a comprehensive database of multiple protein structure alignments (DBALI, http://salilab.org/dbali) as well as web servers for automated comparative modeling with MODPIPE (MODWEB, http://salilab. org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb).
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Affiliation(s)
- Ursula Pieper
- Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California San Francisco, San Francisco, CA 94143-2240, USA
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17
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Kniewel R, Buglino JA, Shen V, Chadha T, Beckwith A, Lima CD. Structural analysis of Saccharomyces cerevisiae myo-inositol phosphate synthase. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2003; 2:129-34. [PMID: 12836703 DOI: 10.1023/a:1021293408654] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The New York Structural Genomics Research Consortium has targeted highly conserved but uncharacterized enzyme families for structure determination. As part of this effort, the 2.65-A crystal structure has been determined for Saccharomyces cerevisiae myo-inositol 1-phosphate synthase (MIP), an essential enzyme that catalyzes critical steps in inositol biosynthesis. The structure determination of four independent monomers in the asymmetric unit (240 kDa) reveals atomic details and residue composition for the partially closed NAD-containing active sites in apo-configuration. The structure further reveals extensive interactions involved in tetrameric assembly of the enzyme complex.
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Affiliation(s)
- Ryan Kniewel
- Biochemistry Department and Structural Biology Program, Weill Medical College of Cornell University, New York, NY 10021, USA
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18
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Padyana AK, Burley SK. Crystal structure of shikimate 5-dehydrogenase (SDH) bound to NADP: insights into function and evolution. Structure 2003; 11:1005-13. [PMID: 12906831 DOI: 10.1016/s0969-2126(03)00159-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structure of Methanococcus jannaschii shikimate 5-dehydrogenase (MjSDH) bound to the cofactor nicotinamide adenine dinucleotide phosphate (NADP) has been determined at 2.35 A resolution. Shikimate 5-dehydrogenase (SDH) is responsible for NADP-dependent catalysis of the fourth step in shikimate biosynthesis, which is essential for aromatic amino acid metabolism in bacteria, microbial eukaryotes, and plants. The structure of MjSDH is a compact alpha/beta sandwich with two distinct domains, responsible for binding substrate and the NADP cofactor, respectively. A phylogenetically conserved deep cleft on the protein surface corresponds to the enzyme active site. The structure reveals a topologically new domain fold within the N-terminal segment of the polypeptide chain, which binds substrate and supports dimerization. Insights gained from homology modeling and sequence/structure comparisons suggest that the SDHs represent a unique class of dehydrogenases. The structure provides a framework for further investigation to discover and develop novel inhibitors targeting this essential enzyme.
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Affiliation(s)
- Anil K Padyana
- Laboratories of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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19
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Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A. Tools for comparative protein structure modeling and analysis. Nucleic Acids Res 2003; 31:3375-80. [PMID: 12824331 PMCID: PMC168950 DOI: 10.1093/nar/gkg543] [Citation(s) in RCA: 346] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB, a web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER; MODLOOP, a web server for automated loop modeling that relies on MODELLER; MOULDER, a CPU intensive protocol of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure; MODVIEW, a Netscape plugin for Linux that integrates viewing of multiple sequences and structures; and SNPWEB, a web server for structure-based prediction of the functional impact of a single amino acid substitution.
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Affiliation(s)
- Narayanan Eswar
- Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143-2240, USA
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20
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Hillisch A, Hilgenfeld R. The role of protein 3D-structures in the drug discovery process. EXS 2003:157-81. [PMID: 12613176 DOI: 10.1007/978-3-0348-7997-2_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
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21
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Ray SS, Bonanno JB, Chen H, de Lencastre H, Wu S, Tomasz A, Burley SK. X-ray structure of an M. jannaschii DNA-binding protein: implications for antibiotic resistance in S. aureus. Proteins 2003; 50:170-3. [PMID: 12471609 DOI: 10.1002/prot.10272] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Soumya S Ray
- Laboratory of Molecular Biophysics, Rockefeller University, New York, New York 10021, USA
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22
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Abstract
The current status of research on the structure, regulation, mechanism and importance of Rubisco activase is reviewed. The activase is now recognized to be a member of the AAA(+) family, whose members participate in macromolecular complexes that perform diverse chaperone-like functions. The conserved nucleotide-binding domain of AAA(+) family members appears to have a common fold that when applied to the activase is generally consistent with previous site-directed mutagenesis studies of the activase. Regulation of the activase in species containing both isoforms can occur via redox changes in the carboxy-terminus of the larger isoform, mediated by thioredoxin-f, which alters the response of activase to the ratio of ADP to ATP in the stroma. Studies of Rubisco activation in transgenic Arabidopsis plants demonstrated that light modulation is dependent on redox regulation of the larger isoform, providing a model for the regulation in other species. Further insights into the mechanism of the activase have emerged from an analysis of the crystal structures of Rubisco conformational variants and the identification of Rubisco residues that confer specificity in its interaction with the activase. The physiological importance of the activase is reinforced by recent studies indicating that it plays a vital role in the response of photosynthesis to temperature. Rubisco activase is one of a new type of chaperone, which in this case functions to promote and maintain the catalytic activity of Rubisco.
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Affiliation(s)
- Archie R Portis
- Photosynthesis Research Unit, Agricultural Research Service, United States Department of Agriculture, and Departments of Crop Sciences and Plant Biology, University of Illinois, Urbana, Illinois, 61801, USA,
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23
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Abstract
High-throughput sequencing of human genomes and those of important model organisms (mouse, Drosophila melanogaster, Caenorhabditis elegans, fungi, archaea) and bacterial pathogens has laid the foundation for another "big science" initiative in biology. Together, X-ray crystallographers, nuclear magnetic resonance (NMR) spectroscopists, and computational biologists are pursuing high-throughput structural studies aimed at developing a comprehensive three-dimensional view of the protein structure universe. The new science of structural genomics promises more than 10,000 experimental protein structures and millions of calculated homology models of related proteins. The evolutionary underpinnings and technological challenges of automating target selection, protein expression and purification, sample preparation, NMR and X-ray data measurement/analysis, homology modeling, and structure/function annotation are discussed in detail. An informative case study from one of the structural genomics centers funded by the National Institutes of Health and the National Institute of General Medical Sciences (NIH/NIGMS) demonstrates how this experimental/computational pipeline will reveal important links between form and function in biology and provide new insights into evolution and human health and disease.
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Affiliation(s)
- Stephen K Burley
- Howard Hughes Medical Institute, Laboratories of Molecular Biophysics, The Rockefeller University, New York New York 10021, USA.
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24
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Deaconescu AM, Roll-Mecak A, Bonanno JB, Gerchman SE, Kycia H, Studier FW, Burley SK. X-ray structure of Saccharomyces cerevisiae homologous mitochondrial matrix factor 1 (Hmf1). Proteins 2002; 48:431-6. [PMID: 12112709 DOI: 10.1002/prot.10151] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Alexandra M Deaconescu
- Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York, USA
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25
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Romanowski MJ, Bonanno JB, Burley SK. Crystal structure of the Streptococcus pneumoniae phosphomevalonate kinase, a member of the GHMP kinase superfamily. Proteins 2002; 47:568-71. [PMID: 12001237 DOI: 10.1002/prot.10118] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Michael J Romanowski
- Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York, USA
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26
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Romanowski MJ, Bonanno JB, Burley SK. Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold. Proteins 2002; 47:563-7. [PMID: 12001236 DOI: 10.1002/prot.10121] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Michael J Romanowski
- Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York
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27
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Fiser A, Feig M, Brooks CL, Sali A. Evolution and physics in comparative protein structure modeling. Acc Chem Res 2002; 35:413-21. [PMID: 12069626 DOI: 10.1021/ar010061h] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
From a physical perspective, the native structure of a protein is a consequence of physical forces acting on the protein and solvent atoms during the folding process. From a biological perspective, the native structure of proteins is a result of evolution over millions of years. Correspondingly, there are two types of protein structure prediction methods, de novo prediction and comparative modeling. We review comparative protein structure modeling and discuss the incorporation of physical considerations into the modeling process. A good starting point for achieving this aim is provided by comparative modeling by satisfaction of spatial restraints. Incorporation of physical considerations is illustrated by an inclusion of solvation effects into the modeling of loops.
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Affiliation(s)
- András Fiser
- Laboratory of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
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28
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Romanowski MJ, Burley SK. Crystal structure of the Escherichia coli shikimate kinase I (AroK) that confers sensitivity to mecillinam. Proteins 2002; 47:558-62. [PMID: 12001235 DOI: 10.1002/prot.10099] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Michael J Romanowski
- Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York
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29
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Burley SK, Bonanno JB. Structural genomics of proteins from conserved biochemical pathways and processes. Curr Opin Struct Biol 2002; 12:383-91. [PMID: 12127459 DOI: 10.1016/s0959-440x(02)00330-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
During the past year, X-ray crystallographers and solution NMR spectroscopists have made significant progress towards the complete structural characterization of conserved biochemical pathways and processes. Some of these advances were made in the context of nascent structural genomics programs, which promise to accelerate structural studies of biologically and medically important proteins. The results of high-throughput protein production, crystallization, structure determination, homology modeling and functional annotation published by two such programs have provided insight into the evolution and function of enzymes in the isoprenoid biosynthesis and ribulose monophosphate pathways.
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Affiliation(s)
- Stephen K Burley
- Howard Hughes Medical Institute, Laboratories of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.
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30
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Romanowski MJ, Gibney SA, Burley SK. Crystal structure of the Escherichia coli SbmC protein that protects cells from the DNA replication inhibitor microcin B17. Proteins 2002; 47:403-7. [PMID: 11948793 DOI: 10.1002/prot.10102] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Michael J Romanowski
- Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York 10021, USA
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31
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Campodonico E, Schwer B. ATP-dependent remodeling of the spliceosome: intragenic suppressors of release-defective mutants of Saccharomyces cerevisiae Prp22. Genetics 2002; 160:407-15. [PMID: 11861548 PMCID: PMC1461984 DOI: 10.1093/genetics/160.2.407] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The essential splicing factor Prp22 is a DEAH-box helicase that catalyzes the release of mRNA from the spliceosome. ATP hydrolysis by Prp22 is necessary but not sufficient for spliceosome disassembly. Previous work showed that mutations in motif III (635SAT637) of Prp22 that uncouple ATP hydrolysis from spliceosome disassembly lead to severe cold-sensitive (cs) growth defects and to impaired RNA unwinding activity in vitro. The cs phenotype of S635A (635AAT) can be suppressed by intragenic mutations that restore RNA unwinding. We now report the isolation and characterization of new intragenic mutations that suppress the cold-sensitive growth phenotypes of the T637A motif III mutation (SAA), the H606A mutation in the DEAH-box (DEAA), and the R805A mutation in motif VI (804QAKGRAGR811). Whereas the T637A and H606A proteins are deficient in releasing mRNA from the spliceosome at nonpermissive temperature in vitro, the suppressor proteins have recovered mRNA release activity. To address the mechanisms of suppression, we tested ATPase and helicase activities of Prp22 suppressor mutant proteins and found that the ability to unwind a 25-bp RNA duplex was not restored in every case. This finding suggests that release of mRNA from the spliceosome is less demanding than unwinding of a 25-bp duplex RNA; the latter reaction presumably reflects the result of several successive cycles of ATP binding, hydrolysis, and unwinding. Increasing the reaction temperature allows H606A and T637A to effect mRNA release in vitro, but does not restore RNA unwinding by T637A.
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Affiliation(s)
- Eva Campodonico
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York 10021, USA
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32
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Kawabata T, Fukuchi S, Homma K, Ota M, Araki J, Ito T, Ichiyoshi N, Nishikawa K. GTOP: a database of protein structures predicted from genome sequences. Nucleic Acids Res 2002; 30:294-8. [PMID: 11752318 PMCID: PMC99104 DOI: 10.1093/nar/30.1.294] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Large-scale genome projects generate an unprecedented number of protein sequences, most of them are experimentally uncharacterized. Predicting the 3D structures of sequences provides important clues as to their functions. We constructed the Genomes TO Protein structures and functions (GTOP) database, containing protein fold predictions of a huge number of sequences. Predictions are mainly carried out with the homology search program PSI-BLAST, currently the most popular among high-sensitivity profile search methods. GTOP also includes the results of other analyses, e.g. homology and motif search, detection of transmembrane helices and repetitive sequences. We have completed analyzing the sequences of 41 organisms, with the number of proteins exceeding 120 000 in total. GTOP uses a graphical viewer to present the analytical results of each ORF in one page in a 'color-bar' format. The assigned 3D structures are presented by Chime plug-in or RasMol. The binding sites of ligands are also included, providing functional information. The GTOP server is available at http://spock.genes.nig.ac.jp/~genome/gtop.html.
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Affiliation(s)
- Takeshi Kawabata
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, 1-111 Yata, Mishima, Shizuoka 411-8540, Japan
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33
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Pieper U, Eswar N, Stuart AC, Ilyin VA, Sali A. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res 2002; 30:255-9. [PMID: 11752309 PMCID: PMC99112 DOI: 10.1093/nar/30.1.255] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2001] [Revised: 10/02/2001] [Accepted: 10/02/2001] [Indexed: 11/12/2022] Open
Abstract
MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAST, IMPALA and MODELLER. MODBASE uses the MySQL relational database management system for flexible and efficient querying, and the MODVIEW Netscape plugin for viewing and manipulating multiple sequences and structures. It is updated regularly to reflect the growth of the protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different datasets. The largest dataset contains models for domains in 304 517 out of 539 171 unique protein sequences in the complete TrEMBL database (23 March 2001); only models based on significant alignments (PSI-BLAST E-value < 10(-4)) and models assessed to have the correct fold are included. Other datasets include models for target selection and structure-based annotation by the New York Structural Genomics Research Consortium, models for prediction of genes in the Drosophila melanogaster genome, models for structure determination of several ribosomal particles and models calculated by the MODWEB comparative modeling web server.
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Affiliation(s)
- Ursula Pieper
- Laboratories of Molecular Biophysics, The Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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Bertini I, Luchinat C, Provenzani A, Rosato A, Vasos PR. Browsing gene banks for Fe2S2 ferredoxins and structural modeling of 88 plant-type sequences: an analysis of fold and function. Proteins 2002; 46:110-27. [PMID: 11746708 DOI: 10.1002/prot.10009] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
One-hundred-and-seventy-nine sequences of Fe2S2 ferredoxins and ferredoxin precursors were identified in and retrieved from currently available protein and cDNA databases. On the basis of their cluster-binding patterns, these sequences were divided into three groups: those containing the CX4CX2CXnC pattern (plant-type ferredoxins), those with the CX5CX2CXnC pattern (adrenodoxins), and those with a different pattern. These three groups contain, respectively, 139, 36, and 4 sequences. After excluding ferredoxin precursors in the first group, two subgroups were identified, again based on their cluster-binding patterns: 88 sequences had the CX4CX2CX29C pattern, and 29 had the CX4CX2CXmC (m not equal 29) pattern. The structures of the 88 ferredoxins with the CX4CX2CX29C pattern were modeled based on the available experimental structures of nine proteins within this same group. The modeling procedure was tested by building structural models for the ferredoxins with known structures. The models resulted, on average, in being within 1 A of the backbone root-mean-square deviation from the corresponding experimental structures. In addition, these structural models were shown to be of high quality by using assessment procedures based on energetic and stereochemical parameters. Thus, these models formed a reliable structural database for this group of ferredoxins, which is meaningful within the framework of current structural genomics efforts. From the analysis of the structural database generated it was observed that the secondary structural elements and the overall three-dimensional structures are maintained throughout the superfamily. In particular, the residues in the hydrophobic core of the protein were found to be either absolutely conserved or conservatively substituted. In addition, certain solvent-accessible charged groups, as well as hydrophobic groups, were found to be conserved to the same degree as the core residues. The patterns of conservation of exposed residues identified the regions of the protein that are critical for its function in electron transfer. An extensive analysis of protein-protein interactions is now possible. Some conserved interactions between residues have been identified and related to structural and/or functional features. All this information could not be obtained from the analyses of the primary sequences alone. Finally, the analysis of the sequences of the related subgroup featuring the CX4CX2CXmC (m not equal 29) cluster-binding pattern in the light of the structural and functional insights provided by the inspection of the mentioned structural database affords some hints on the functional features of ferredoxins belonging to this subgroup.
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Affiliation(s)
- Ivano Bertini
- Centro di Risonanze Magnetiche, University of Florence, Sesto Fiorentino, Italy.
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35
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Bonanno JB, Edo C, Eswar N, Pieper U, Romanowski MJ, Ilyin V, Gerchman SE, Kycia H, Studier FW, Sali A, Burley SK. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. Proc Natl Acad Sci U S A 2001; 98:12896-901. [PMID: 11698677 PMCID: PMC60796 DOI: 10.1073/pnas.181466998] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
X-ray structures of two enzymes in the sterol/isoprenoid biosynthesis pathway have been determined in a structural genomics pilot study. Mevalonate-5-diphosphate decarboxylase (MDD) is a single-domain alpha/beta protein that catalyzes the last of three sequential ATP-dependent reactions which convert mevalonate to isopentenyl diphosphate. Isopentenyl disphosphate isomerase (IDI) is an alpha/beta metalloenzyme that catalyzes interconversion of isopentenyl diphosphate and dimethylallyl diphosphate, which condense in the next step toward synthesis of sterols and a host of natural products. Homology modeling of related proteins and comparisons of the MDD and IDI structures with two other experimentally determined structures have shown that MDD is a member of the GHMP superfamily of small-molecule kinases and IDI is similar to the nudix hydrolases, which act on nucleotide diphosphatecontaining substrates. Structural models were produced for 379 proteins, encompassing a substantial fraction of both protein superfamilies. All three enzymes responsible for synthesis of isopentenyl diphosphate from mevalonate (mevalonate kinase, phosphomevalonate kinase, and MDD) share the same fold, catalyze phosphorylation of chemically similar substrates (MDD decarboxylation involves phosphorylation of mevalonate diphosphate), and seem to have evolved from a common ancestor. These structures and the structural models derived from them provide a framework for interpreting biochemical function and evolutionary relationships.
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Affiliation(s)
- J B Bonanno
- Laboratories of Molecular Biophysics, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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36
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Spahn CM, Beckmann R, Eswar N, Penczek PA, Sali A, Blobel G, Frank J. Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions. Cell 2001; 107:373-86. [PMID: 11701127 DOI: 10.1016/s0092-8674(01)00539-6] [Citation(s) in RCA: 382] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A cryo-EM reconstruction of the translating yeast 80S ribosome was analyzed. Computationally separated rRNA and protein densities were used for docking of appropriately modified rRNA models and homology models of yeast ribosomal proteins. The core of the ribosome shows a remarkable degree of conservation. However, some significant differences in functionally important regions and dramatic changes in the periphery due to expansion segments and additional ribosomal proteins are evident. As in the bacterial ribosome, bridges between the subunits are mainly formed by RNA contacts. Four new bridges are present at the periphery. The position of the P site tRNA coincides precisely with its prokaryotic counterpart, with mainly rRNA contributing to its molecular environment. This analysis presents an exhaustive inventory of an eukaryotic ribosome at the molecular level.
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MESH Headings
- Base Sequence
- Binding Sites
- Cryoelectron Microscopy/methods
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- Saccharomyces cerevisiae/genetics
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Affiliation(s)
- C M Spahn
- Howard Hughes Medical Institute, Health Research Inc., Albany, NY 12201, USA
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37
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Abstract
Genome sequencing projects are producing linear amino acid sequences, but full understanding of the biological role of these proteins will require knowledge of their structure and function. Although experimental structure determination methods are providing high-resolution structure information about a subset of the proteins, computational structure prediction methods will provide valuable information for the large fraction of sequences whose structures will not be determined experimentally. The first class of protein structure prediction methods, including threading and comparative modeling, rely on detectable similarity spanning most of the modeled sequence and at least one known structure. The second class of methods, de novo or ab initio methods, predict the structure from sequence alone, without relying on similarity at the fold level between the modeled sequence and any of the known structures. In this Viewpoint, we begin by describing the essential features of the methods, the accuracy of the models, and their application to the prediction and understanding of protein function, both for single proteins and on the scale of whole genomes. We then discuss the important role that protein structure prediction methods play in the growing worldwide effort in structural genomics.
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Affiliation(s)
- D Baker
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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38
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Xu D, Baburaj K, Peterson CB, Xu Y. Model for the three-dimensional structure of vitronectin: predictions for the multi-domain protein from threading and docking. Proteins 2001; 44:312-20. [PMID: 11455604 DOI: 10.1002/prot.1096] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The structure of vitronectin, an adhesive protein that circulates in high concentrations in human plasma, was predicted through a combination of computational methods and experimental approaches. Fold recognition and sequence-structure alignment were performed using the threading program PROSPECT for each of three structural domains, i.e., the N-terminal somatomedin B domain (residues 1-53), the central region that folds into a four-bladed beta-propeller domain (residues 131-342), and the C-terminal heparin-binding domain (residues 347-459). The atomic structure of each domain was generated using MODELLER, based on the alignment obtained from threading. Docking experiments between the central and C-terminal domains were conducted using the program GRAMM, with limits on the degrees of freedom from a known inter-domain disulfide bridge. The docked structure has a large inter-domain contact surface and defines a putative heparin-binding groove at the inter-domain interface. We also docked heparin together with the combined structure of the central and C-terminal domains, using GRAMM. The predictions from the threading and docking experiments are consistent with experimental data on purified plasma vitronectin pertaining to protease sensitivity, ligand-binding sites, and buried cysteines.
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Affiliation(s)
- D Xu
- Computational Biology Section, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6480, USA.
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39
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Kolinski A, Betancourt MR, Kihara D, Rotkiewicz P, Skolnick J. Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins 2001; 44:133-49. [PMID: 11391776 DOI: 10.1002/prot.1080] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An improved generalized comparative modeling method, GENECOMP, for the refinement of threading models is developed and validated on the Fischer database of 68 probe-template pairs, a standard benchmark used to evaluate threading approaches. The basic idea is to perform ab initio folding using a lattice protein model, SICHO, near the template provided by the new threading algorithm PROSPECTOR. PROSPECTOR also provides predicted contacts and secondary structure for the template-aligned regions, and possibly for the unaligned regions by garnering additional information from other top-scoring threaded structures. Since the lowest-energy structure generated by the simulations is not necessarily the best structure, we employed two structure-selection protocols: distance geometry and clustering. In general, clustering is found to generate somewhat better quality structures in 38 of 68 cases. When applied to the Fischer database, the protocol does no harm and in a significant number of cases improves upon the initial threading model, sometimes dramatically. The procedure is readily automated and can be implemented on a genomic scale.
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Affiliation(s)
- A Kolinski
- Laboratory of Computational Genomics, Donald Danforth Plant Science Center, St. Louis, Missouri 63141, USA
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40
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Abstract
The most important advances in the field of genome annotation over the past two years involve the use of cDNA sequences, protein structures and gene expression data to predict genes. These types of information not only improve gene identification, but they also give insights into variation in gene structure and function.
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Affiliation(s)
- T Gaasterland
- Laboratory of Computational Genomics, 1230 York Avenue, Rockefeller University, New York, New York 10021, USA.
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41
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D'Alfonso G, Tramontano A, Lahm A. Structural conservation in single-domain proteins: implications for homology modeling. J Struct Biol 2001; 134:246-56. [PMID: 11551183 DOI: 10.1006/jsbi.2001.4351] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Large-scale sequencing projects are widening the gap between the known protein universe and the fraction for which structural information has been experimentally obtained. Through the application of homology (comparative) modeling and more general structure prediction techniques, this gap can, however, be narrowed, providing indirect structural information for a considerable number of proteins. Moreover, the estimated number of existing protein folds seems to be limited and many of these yet unknown folds should be discovered by dedicated large-scale structural genomics projects. Within this perspective, homology (comparative) modeling will gain in importance, as will the use of models derived by this technique. Here we discuss how well a sequence alignment, the most common starting point for generating a model, reflects the structural conservation between homologous proteins and we show that sequence information is able to direct construction of acceptable models as far as the structural core is concerned. We also show here that the regions surrounding insertions and deletions are much less conserved than the core and discuss the implications of this observation for loop modeling.
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42
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Heger A, Holm L. Towards a covering set of protein family profiles. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2001; 73:321-37. [PMID: 11063778 DOI: 10.1016/s0079-6107(00)00013-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Evolutionary classification leads to an economical description of the protein sequence universe because attributes of function and structure are inherited in protein families. Efficient strategies of functional and structural genomics therefore target one representative from each family. Enumerating all families and establishing family membership consistently based on sequence similarities are nontrivial computational problems. Emerging concepts and caveats of global sequence clustering are reviewed. Explicit multiple alignments coupled with neighbourhood analysis lead to domain segmentation, and hierarchical unification helps to resolve conflicts and validate clusters. Eventually, every part of every sequence will be assigned to a domain family which is uniquely associated with a fold and a molecular function.
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Affiliation(s)
- A Heger
- Structural Genomics Group, EMBL-EBI, 10 1SD, Cambridge CB, UK
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43
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Blundell TL, Mizuguchi K. Structural genomics: an overview. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2001; 73:289-95. [PMID: 11063776 DOI: 10.1016/s0079-6107(00)00008-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- T L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, 2 1GA, Cambridge CB, UK.
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44
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Martí-Renom MA, Stuart AC, Fiser A, Sánchez R, Melo F, Sali A. Comparative protein structure modeling of genes and genomes. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2001; 29:291-325. [PMID: 10940251 DOI: 10.1146/annurev.biophys.29.1.291] [Citation(s) in RCA: 2337] [Impact Index Per Article: 101.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. The number of protein sequences that can be modeled and the accuracy of the predictions are increasing steadily because of the growth in the number of known protein structures and because of the improvements in the modeling software. Further advances are necessary in recognizing weak sequence-structure similarities, aligning sequences with structures, modeling of rigid body shifts, distortions, loops and side chains, as well as detecting errors in a model. Despite these problems, it is currently possible to model with useful accuracy significant parts of approximately one third of all known protein sequences. The use of individual comparative models in biology is already rewarding and increasingly widespread. A major new challenge for comparative modeling is the integration of it with the torrents of data from genome sequencing projects as well as from functional and structural genomics. In particular, there is a need to develop an automated, rapid, robust, sensitive, and accurate comparative modeling pipeline applicable to whole genomes. Such large-scale modeling is likely to encourage new kinds of applications for the many resulting models, based on their large number and completeness at the level of the family, organism, or functional network.
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Affiliation(s)
- M A Martí-Renom
- Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, Rockefeller University, New York, NY 10021, USA
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45
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Abstract
The prediction of protein structure, based primarily on sequence and structure homology, has become an increasingly important activity. Homology models have become more accurate and their range of applicability has increased. Progress has come, in part, from the flood of sequence and structure information that has appeared over the past few years, and also from improvements in analysis tools. These include profile methods for sequence searches, the use of three-dimensional structure information in sequence alignment and new homology modeling tools, specifically in the prediction of loop and side-chain conformations. There have also been important advances in understanding the physical chemical basis of protein stability and the corresponding use of physical chemical potential functions to identify correctly folded from incorrectly folded protein conformations.
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Affiliation(s)
- B Al-Lazikani
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, 630 West 168th Street, New York, NY 10032, USA
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46
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Abstract
Functional analysis of the proteins discovered in fully sequenced genomes represent the next major challenge of life science research. Computational methods play an increasingly important role in this activity. Among them, comparative protein modelling will play a major role in this challenge, especially in the light of the Structural Genomics programmes about to be started around the world. In recent years, much progress has been made in automating these methods, enabling the production of models for genome scale problems. In this review we discuss how protein models can be applied to functional analysis, as well as some of the current issues and limitations inherent to these methods.
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Affiliation(s)
- M C Peitsch
- Glaxo Wellcome Experimental Research, Plan-les-Ouates/GE, Switzerland.
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47
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Crawford ME, Cusick ME, Garrels JI. Databases and knowledge resources for proteomics research. Trends Biotechnol 2000. [DOI: 10.1016/s0167-7799(00)00012-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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