Molecular docking uncovers TSPY binds more efficiently with eEF1A2 compared to eEF1A1

Abstract

Testis-specific protein, Y-encoded (TSPY) binds to eukaryotic translation elongation factor 1 alpha (eEF1A) at its SET/NAP domain that is essential for the elongation during protein synthesis implicated with normal spermatogenesis. The eEF1A exists in two forms, eEF1A1 (alpha 1) and eEF1A2 (alpha 2), encoded by separate loci. Despite critical interplay of the TSPY and eEF1A proteins, literature remained silent on the residues playing significant roles during such interactions. We deduced 3D structures of TSPY and eEF1A variants by comparative modeling (Modeller 9.13) and assessed protein–protein interactions employing HADDOCK docking. Pairwise alignment using EMBOSS Needle for eEF1A1 and eEF1A2 proteins revealed high degree (~92%) of homology. Efficient binding of TSPY with eEF1A2 as compared to eEF1A1 was observed, in spite of the occurrence of significant structural similarities between the two variants. We also detected strong interactions of domain III followed by domains II and I of both eEF1A variants with TSPY. In the process, seven interacting residues of TSPY’s NAP domain namely, Asp 175, Glu 176, Asp 179, Tyr 183, Asp 240, Glu 244, and Tyr 246 common to both eEF1A variants were detected. Additionally, six lysine residues observed in eEF1A2 suggest their possible role in TSPY–eEF1A2 complex formation essential for germ cell development and spermatogenesis. Thus, more efficient binding of TSPY with eEF1A2 as compared to that of eEF1A1 established autonomous functioning of these two variants. Studies on mutated protein following similar approach would uncover the causative obstruction, between the interacting partners leading to deeper understanding on the structure–function relationship.

Keywords:

• comparative modeling
• 3D structure
• binding sites
• protein docking
• protein–protein interactions

Acknowledgments

SA acknowledges award of the J.C. Bose National Fellowship by DST, New Delhi and equipment donation from Alexander Von Humboldt Foundation, Bonn, Germany. Technical assistance from Khem Singh Negi is acknowledged. We thank Debasisa Mohanty for his critical comments on the manuscript. We express our deep sense of appreciation to the anonymous referees for their valuable inputs on our manuscript, which indeed have meliorated its quality.

Additional information

Funding

Funding. This work was supported by a core grant from the Department of Biotechnology (DBT) to the National Institute of Immunology, New Delhi and research grants nos. BT/PR11805/MED/12/424/2009, BT/PR14102/AAQ/01/438/2010 from DBT, New Delhi and no.SR/SO/AS-115/2012 from the Department of Science and Technology (DST), New Delhi to SA.