Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different

De, Subhajyoti; Krishnadev, O.; Srinivasan, N.; Rekha, N.
January 2005
BMC Structural Biology;2005, Vol. 5, p15
Academic Journal
Background: A polypeptide chain of a protein-protein complex is said to be obligatory if it is bound to another chain throughout its functional lifetime. Such a chain might not adopt the native fold in the unbound form. A non-obligatory polypeptide chain associates with another chain and dissociates upon molecular stimulus. Although conformational changes at the interaction interface are expected, the overall 3-D structure of the non-obligatory chain is unaltered. The present study focuses on protein-protein complexes to understand further the differences between obligatory and non-obligatory interfaces. Results: A non-obligatory chain in a complex of known 3-D structure is recognized by its stable existence with same fold in the bound and unbound forms. On the contrary, an obligatory chain is detected by its existence only in the bound form with no evidence for the native-like fold of the chain in the unbound form. Various interfacial properties of a large number of complexes of known 3-D structures thus classified are comparatively analyzed with an aim to identify structural descriptors that distinguish these two types of interfaces. We report that the interaction patterns across the interfaces of obligatory and non-obligatory components are different and contacts made by obligatory chains are predominantly non-polar. The obligatory chains have a higher number of contacts per interface (20 ± 14 contacts per interface) than non-obligatory chains (13 ± 6 contacts per interface). The involvement of main chain atoms is higher in the case of obligatory chains (16.9 %) compared to non-obligatory chains (11.2 %). The β-sheet formation across the subunits is observed only among obligatory protein chains in the dataset. Apart from these, other features like residue preferences and interface area produce marginal differences and they may be considered collectively while distinguishing the two types of interfaces. Conclusion: These results can be useful in distinguishing the two types of interfaces observed in structures determined in large-scale in the structural genomics initiatives, especially for those multi-component protein assemblies for which the biochemical characterization is incomplete.


Related Articles

  • Accurate multiplex gene synthesis from programmable DNA microchips. Jingdong Tian; Hui Gong; Nijing Sheng; Xiaochuan Zhou; Erdogan Gulari; Xiaolian Gao; Church, George // Nature;12/23/2004, Vol. 432 Issue 7020, p1050 

    Testing the many hypotheses from genomics and systems biology experiments demands accurate and cost-effective gene and genome synthesis. Here we describe a microchip-based technology for multiplex gene synthesis. Pools of thousands of‘construction’oligonucleotides and tagged...

  • Chemical Genomics Is the "Big Tent" of Drug Discovery. DePalma, Angelo // Drug Discovery & Development;Oct2004, Vol. 7 Issue 10, p51 

    Discusses the significance of chemical genomics in drug discovery. Popularity of classical chemical genomics; Terminologies related to chemical genomics; Detection of targets for drugs rather than drugs for targets; Screening of proteins; Fragment-based approach. INSETS: Back to Nature;NH Funds...

  • Partitioning clustering algorithms for protein sequence data sets. Fayech, Sondes; Essoussi, Nadia; Limam, Mohamed // BioData Mining;2009, Vol. 2, p1 

    Background: Genome-sequencing projects are currently producing an enormous amount of new sequences and cause the rapid increasing of protein sequence databases. The unsupervised classification of these data into functional groups or families, clustering, has become one of the principal research...

  • Genotyping of Three Single Nucleotide Polymorphisms Following Whole Genome Preamplification of DNA Collected from Buccal Cells. Haaberstick, Brett C.; Smolen, Andrew // Behavior Genetics;Sep2004, Vol. 34 Issue 5, p541 

    Collection of genomic DNA from buccal cells is a simple and convenient procedure for genotyping individuals. One disadvantage is that the amount of genomic DNA may be inadequate for genotyping projects that require a large number of determinations per sample. Primer Extension Preamplification...

  • Genomics: Profiling transcriptional heterogeneity.  // Nature Methods;Jul2013, Vol. 10 Issue 7, p607 

    The article cites a new study that developed transcript isoform sequencing to profile isoform diversity.

  • Population genomics: Triallelic sites and demographic history. Flintoft, Louisa // Nature Reviews Genetics;Jan2014, Vol. 15 Issue 1, p2 

    The article highlights a study on population genetic, which is the site-frequency spectrum, describing the distribution of allele frequencies in the population.

  • Structure-based function prediction: approaches and applications. Gherardini, Pier Federico; Helmer-Citterich, Manuela // Briefings in Functional Genomics & Proteomics;Jul2008, Vol. 7 Issue 4, p291 

    The ever increasing number of protein structures determined by structural genomic projects has spurred much interest in the development of methods for structure-based function prediction. Existing methods can be roughly classified in two groups: some use a comparative approach looking for the...

  • Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Kulpa, Deanna A.; Moran, John V. // Nature Structural & Molecular Biology;Jul2006, Vol. 13 Issue 7, p655 

    LINE-1 retrotransposons (L1s) constitute ∼17% of human DNA, and their activity continues to affect genome evolution. Retrotransposition-competent human L1s encode two proteins required for their mobility (ORF1p and ORF2p); however, biochemical activities associated with ORF2p have been...

  • Accurate identification of orthologous segments among multiple genomes. Hachiya, Tsuyoshi; Osana, Yasunori; Popendorf, Kris; Sakakibara, Yasubumi // Bioinformatics;Apr2009, Vol. 25 Issue 7, p853 

    Motivation: The accurate detection of orthologous segments (also referred to as syntenic segments) plays a key role in comparative genomics, as it is useful for inferring genome rearrangement scenarios and computing whole-genome alignments. Although a number of algorithms for detecting...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics