Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain.

Arvind Ramanathan,Akash Parvatikar,Srinivas C Chennubhotla,Sangita C Sinha,Yang Mei

doi:10.3390/biom10091308

Abstract

Viral BCL2 proteins (vBCL2s) help to sustain chronic infection of host proteins to inhibit apoptosis and autophagy. However, details of conformational changes in vBCL2s that enable binding to BH3Ds remain unknown. Using all-atom, multiple microsecond-long molecular dynamic simulations (totaling 17 s) of the murine -herpesvirus 68 vBCL2 (M11), and statistical inference techniques, we show that regions of M11 transiently unfold and refold upon binding of the BH3D. Further, we show that this partial unfolding/refolding within M11 is mediated by a network of hydrophobic interactions, which includes residues that are 10 Å away from the BH3D binding cleft. We experimentally validate the role of these hydrophobic interactions by quantifying the impact of mutating these residues on binding to the Beclin1/BECN1 BH3D, demonstrating that these mutations adversely affect both protein stability and binding. To our knowledge, this is the first study detailing the binding-associated conformational changes and presence of long-range interactions within vBCL2s.

Highlights

Human and other vertebrate cells encode B-cell lymphoma 2 proteins, which are important regulators of homeostatic pathways, such as apoptosis and autophagy [1,2,3,4]
We carried out molecular dynamics (MD) simulations using three systems in order to gain insights into BCL2 homology 3 domains (BH3Ds)-binding associated conformational changes in M11: (1) 2ABO-apo: which refers to the simulation of apo-M11 initiated from the unliganded M11 NMR ensemble (PDB ID 2ABO [42]); (2) 3DVU-apo: which refers to the simulation started from the holo-M11 X-ray crystal structure (PDB ID 3DVU [19] chain A), but with the BECN1 BH3D removed from the binding cleft; and, (3) 3DVU-holo: which refers to the simulation of holo M11, with the BECN1 BH3D bound to the M11 binding cleft (PDB ID 3DVU chains A and B)
Within oncogenic viruses, targeting anti-apoptotic/anti-autophagic Viral BCL2 proteins (vBCL2s) offers strategic benefits, since drugs can target a critical part of the viral life-cycle, namely viral reactivation from latency and proliferation [29,52]

Summary

Introduction

Human and other vertebrate cells encode B-cell lymphoma 2 proteins (cBCL2s), which are important regulators of homeostatic pathways, such as apoptosis and autophagy [1,2,3,4] Oncogenic viruses, such as Epstein–Barr virus (EBV), Kaposi’s sarcoma-associated virus (KSHV), and the murine-γ-herpesvirus 68 (γ-HV68), express homologs of cBCL2s [5]. These viral BCL2s (vBCL2s) bind to cellular pro-apoptotic or pro-autophagic proteins to mediate the inhibition of apoptosis and autophagy, thereby supporting the survival of infected host cells [6,7,8,9] and preventing viruses from being destroyed [10]. Designing vBCL2 inhibitors is challenging, because of the high degree of sequence and structural variation amongst vBCL2s and a lack of understanding of the binding-associated conformational changes in vBCL2s

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Conclusion