Evaluation and improvement of multiple sequence methods for protein secondary structure prediction

Cuff, James; Barton, Geoffrey J.

doi:10.1002/(sici)1097-0134(19990301)34:4<508::aid-prot10>3.0.co;2-4

Cited by 615 publications

(534 citation statements)

References 84 publications

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“…Of these, one, Gln-7 to Pro (NS3-Q7P), was designed to disrupt the native structural motif of the first 14 amino acids. The other two substitutions, Arg-8 to Glu and Glu-10 to Ala (NS3-R8E, NS3-E10A), were made in an attempt to maintain the overall protein structure as predicted by using JPRED (30).…”

Section: Site-directed Mutagenesis Of the P11-binding Motif Of Ns3 Andmentioning

confidence: 99%

The membrane trafficking protein calpactin forms a complex with bluetongue virus protein NS3 and mediates virus release

Beaton

Rodrı́guez

Reddy

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

112

120

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Bluetongue virus, an arbovirus of the Orbivirus genus, infects and replicates in both insect and mammalian cells. However, the cytopathic effect (cpe) on each host is very different. Mammalian cells show substantial cpe, most likely a result of the mechanism of virus release, whereas insect cells show little cpe and appear to release virus without cell lysis. Expression analysis of each infected cell type shows one protein, the nonstructural (NS) protein NS3, to be differentially expressed in the different cell types, suggesting it may act in the virus egress pathway. The molecular basis of such an interaction, however, has never been clear. Here, by using yeast two-hybrid analysis, we show that NS3 interacts with a cellular protein p11 (calpactin light chain), part of the annexin II complex that is involved in exocytosis. We map the NS3 region of interaction with p11 to a 13-residue peptide found at the N terminus of the protein and show it effectively competes with p36 (annexin II heavy chain) for p11 ligand binding. Further, we show that the C-terminal domain of NS3 interacts with VP2, the outermost protein of the fully assembled virus particle, suggesting that NS3 forms a bridging molecule that draws assembled virus into contact with the cellular export machinery. Our data describe the first host protein involvement in orbivirus egress and provide new insights into understanding arbovirus interactions with their hosts.I nsect-borne arboviruses (arthropod-borne viruses), such as members of genus Orbivirus, are vectored to vertebrate species by arthropod species (e.g., gnats, mosquitoes, and ticks) and replicate in both hosts. However, whereas in vertebrate host cells these viruses cause severe cell damage, infections of insect cells are often inapparent. Bluetongue virus (BTV), the prototype virus of the genus Orbivirus, is transmitted by Culicoides spp., causing a disease of economical importance in the vertebrate hosts (ruminants) in many parts of the world. Other orbiviruses (14 serogroups within the genus, including African horse sickness virus and Epizootic hemorrhagic disease virus of deer) infect a variety of vertebrates, including humans, often causing severe diseases (1).Unlike the other arboviruses, BTV and other orbiviruses are nonenveloped and lack the glycosylated proteins known to facilitate both virus entry and exit processes. Consequently, orbiviruses are released from the infected cells predominantly by cell lysis (2, 3). However, BTV causes less severe cytopathic effects in insect vector cells despite highly efficient virus replication (4). BTV release from vector cells is nonlytic, and the virus particles leave the infected cell by passage, either individually or in groups, through a locally disrupted plasma membrane (5). However, the exact mechanism of cell-to-cell spread by the virus is not clear, and how the virus controls differential egress in insect and mammalian cells is one of the most intriguing aspects of BTV biology.BTV virions are architecturally complex icosahedral structures c...

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Section: Site-directed Mutagenesis Of the P11-binding Motif Of Ns3 Andmentioning

confidence: 99%

The membrane trafficking protein calpactin forms a complex with bluetongue virus protein NS3 and mediates virus release

Beaton

Rodrı́guez

Reddy

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

112

120

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“…Indeed, by using a combination of techniques such as multiple sequence alignment and neural networks, one can predict the basic secondary structural features, e.g., ␣-helices and ␤-strands, with a confidence that exceeds 70%. [11][12][13][14] Our simplified task could be thought of as a step in the ultimate goal of ab initio tertiary structure prediction. As we shall demonstrate, an important attendant advantage of such a simplified challenge is that it allows one to glean fundamental insights into the protein folding problem.…”

Section: Introductionmentioning

confidence: 99%

Assembly of protein tertiary structures from secondary structures using optimized potentials

et al. 2003

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We present a simulated annealingbased method for the prediction of the tertiary structures of proteins given knowledge of the secondary structure associated with each amino acid in the sequence. The backbone is represented in a detailed fashion whereas the sidechains and pairwise interactions are modeled in a simplified way, following the LINUS model of Srinivasan and Rose. A perceptron-based technique is used to optimize the interaction potentials for a training set of three proteins. For these proteins, the procedure is able to reproduce the tertiary structures to below 3 Å in root mean square deviation (rmsd) from the PDB targets. We present the results of tests on twelve other proteins. For half of these, the lowest energy decoy has a rmsd from the native state below 6 Å and, in 9 out of 12 cases, we obtain decoys whose rmsd from the native states are also well below 5 Å. Proteins 2003;52:155-165.

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“…Therefore, when treated as a binary-class classification problem, the data set contains few positive examples. 2 The set of 513 protein sequences was constructed by [3], which includes almost all the sequences in the RS126 dataset. It contains 84, 119 residues of which 22.7% are β-sheets.…”

Section: Data Sets and Experiments Setupmentioning

confidence: 99%

Exploiting Long-Range Dependencies in Protein β-Sheet Secondary Structure Prediction

Niranjan

2010

Pattern Recognition in Bioinformatics

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Abstract. We investigate if interactions of longer range than typically considered in local protein secondary structure prediction methods can be captured in a simple machine learning framework to improve the prediction of β sheets. We use support vector machines and recursive feature elimination to show that the small signals available in long range interactions can indeed be exploited. The improvement is small but statistically significant on the benchmark datasets we used. We also show that feature selection within a long window and over amino acids at specific positions typically selects amino acids that are shown to be more relevant in the initiation and termination of β-sheet formation.

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Evaluation and improvement of multiple sequence methods for protein secondary structure prediction

Cited by 615 publications

References 84 publications

The membrane trafficking protein calpactin forms a complex with bluetongue virus protein NS3 and mediates virus release

The membrane trafficking protein calpactin forms a complex with bluetongue virus protein NS3 and mediates virus release

Assembly of protein tertiary structures from secondary structures using optimized potentials

Exploiting Long-Range Dependencies in Protein β-Sheet Secondary Structure Prediction

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