Comparative sequence analysis is considered as the first step towards annotating new proteins in genome annotation. However, sequence comparison may lead to creation and propagation of function assignment errors. Thus, it is important to perform a th
The elastic interaction energy between tetragonal zirconia precipitates for different mutual orientations is considered. The results of numerical analysis of this procedure are compared with experimentally observed preferred orientation relationships
The importance of entrepreneurship to a nation development is unneglectable. Malaysian government has carried out various supporting activities to promote entrepreneurial activities in the country. However, the results were less embracing, especially
Value orientations are believed to influence learning in school. We assume that this influence is mediated by the valences attached to specific school subjects. In a questionnaire study (704 students from 36 classes) achievement and well-being value
The paper aims to examine the relationship between Entrepreneurial Orientation (EO), Market Orientation (MO) and performance in University Spin-Offs (USOs). Initially, the paper, assesses the existence of a moderating effect of MO in the relationship
Results of a study investigating the relation between personality traits and ethical-orientation indicate sex is not an good predictor for differences in Machiavellian-, Type A personality- or ethical-orientation. Intelligence is found to be positive
The purpose of this case study is to delve into the complexities of how preservice science teachers’ science teaching orientations, viewed as an interrelated set of beliefs, interact with the other components of pedagogical content knowledge (PCK). E
In two experiments, we tested the hypothesis that increases in the level of interaction between a subject and an apparent stranger would result in a more positive impression of the stranger. The research was conducted in both actual (Experiment 1) an
Promoter strength, or activity, is important in genetic engineering and synthetic biology. A constitutive promoter with a certain strength for one given RNA can often be reused for other RNAs. Therefore, the strength of one promoter is mainly determi
The underlying relationship between functional variables and sequence evolutionary rates is often assessed by partial correlation analysis. However, this strategy is impeded by the difficulty of conducting meaningful statistical analysis using noisy
BMC Systems Biology
The relationship between domain-domain interaction orientation and sequence similarity Emily Jefferson* and Geoffrey Barton Address: School of Life Sciences, University of Dundee, Dundee, UK Email: Emily Jefferson* - [email protected] * Corresponding author
from BioSysBio 2007: Systems Biology, Bioinformatics and Synthetic Biology Manchester, UK. 11–13 January 2007 Published: 8 May 2007 BMC Systems Biology 2007, 1(Suppl 1):S13
BioSysBio 2007: Systems Biology, Bioinformatics, Synthetic Biology
John Cumbers, Xu Gu, Jong Sze WongMeeting abstracts – A single PDF containing all abstracts in this Supplement is available here.http://www.biomedcentral.com/content/pdf/1752-0509-1-S1-info.pdf
In general proteins of similar sequence have a similar structure. We investigate whether a similar correlation exists between sequence identity and domain-domain interaction similarity. Understanding this relationship is important to the study of many aspects of protein-protein interactions, for example, the prediction of interaction information based on homology to complexes observed in structural data. Here the relationship between sequence identity and interaction similarity is investigated with the inclusion of all interactions within a structure and with redundancy filtering based upon normalisation by the pairwise SCOP  family classification of the interacting domains.
The probability that a pair of interactions were observed at the same orientation was determined and plotted against their sequence identity. The results were normalised by the frequency of the pairwise SCOP  family classification. There is a positive correlation between the probability of the same orientation between a pair of interactions and their % sequence identity (Figure 1).
Materials and methods Domain-domain interactions were employed rather than protein-protein interactions as domains can be considered to be the fundamental functional and structural unit of proteins. SCOP  was chosen as the domain classification system. The domain-domain interactions where again obtained from SNAPPI-DB (Structures, iNterfaces and Alignments of Protein-Protein Interactions – DataBase) . The problem of interactions due to crystal packing artefacts was reduced by use of biological units, as predicted by PQS . Domain-domain interaction orientation was determined using an implementation of the iRMSD method described in Aloy et al . The sequence identity between two domains was obtained from the STAMP  alignment output.
Figure The the same probability 1 orientation that aagainst pair of sequence interactions identity are interacting at The probability that a pair of interactions are interacting at the same orientation against sequence identity.
Page 1 of 2 (page number not for citation purposes)
BMC Systems Biology 2007, 1(Suppl 1):S13
Conclusion Even at high sequence identities domain-domain interactions have approx. 20% probability of interacting at a different orientation.
Acknowledgements Emily Jefferson is supported by a BBSRC (UK Biotechnology and Biological Sciences Research Council) studentship.
References 1. 2. 3. 4. 5.
Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540. Henrick K, Thornton JM: PQS: a protein quaternary structure file server. Trends Biochem Sci 1998, 23:358-361. Aloy P, Ceulemans H, Stark A, Russell RB: The relationship between sequence and interaction divergence in proteins. J Mol Biol 2003, 332:989-998. Russell RB, Barton GJ: Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins 1992, 14:309-323. Jefferson ER, Walsh TP, Barton GJ: SNAPPI-DB: A Database and API of Structures, iNterfaces and Alignments for ProteinProtein Interactions. Nucleic Acids Res in press.
Publish with Bio Med Central and every scientist can read your work free of charge "BioMed Central will be the most significant development for disseminating the results of biomedical researc h in our lifetime." Sir Paul Nurse, Cancer Research UK
Your research papers will be: available free of charge to the entire biomedical community peer reviewed and published immediately upon acceptance cited in PubMed and archived on PubMed Central yours — you keep the copyright
Submit your manuscript here: http://www.biomedcentral.com/info/publishing_adv.asp
Page 2 of 2 (page number not for citation purposes)