A study of the structural properties and thermal stability of human Bcl-2 by molecular dynamics simulations

Abstract

The anti-apoptotic B-cell lymphoma 2 (Bcl-2) protein interacts with several proteins that regulate the apoptotic properties of cells. In this research, we conduct several all-atom molecular dynamics (MD) simulations under high-temperature unfolding conditions, from 400 to 800 K, for 25 ns. These simulations were performed using a model of an engineered Bcl-2 human protein (Bcl-2-Δ22Σ3), which lacks 22 C-terminal residues of the transmembrane domain. The aim of this study is to gain insight into the structural behavior of Bcl-2-Δ22Σ3 by mapping the conformational movements involved in Bcl-2 stability and its biological function. To build a Bcl-2-Δ22Σ3 three-dimensional model, the protein core was built by homology modeling and the flexible loop domain (FLD, residues 33-91) by ab initio methods. Further, the entire protein model was refined by MD simulations. Afterwards, the production MD simulations showed that the FLD at 400 and 500 K has several conformations reaching into the protein core, whereas at 600 K some of the alpha-helices were lost. At 800 K, the Bcl-2 core is destabilized suggesting a possible mechanism for protein unfolding, where the alpha helices 1 and 6 were the most stable, and a reduction in the number of hydrogen bonds initially occurs. In conclusion, the structural changes and the internal protein interactions suggest that the core and the FLD are crucial components of Bcl-2 in its function of regulate ng access to the recognition sites of kinases and caspases.

Identification of the antiepileptic racetam binding site in the synaptic vesicle protein 2A by molecular dynamics and docking simulations

“…The results showed that the TM domains reached equilibrium and were likely to be correctly modeled; whereas the regions outside the membrane still remained mobile (also shown by the RMSF values). This is a general occurrence for TM proteins ( Nugent and Jones, 2012 ) and it has been reported for other proteins, such as Bcl-2 ( Ilizaliturri-Flores et al, 2013 ).…”

Exploring the Conformational Space of Bcl-2 Protein Variants: Dynamic Contributions of the Flexible Loop Domain and Transmembrane Region

“…Similar results have been reported in previous reports. The conformational changes observed, showing the propensity of FLD to fold on itself and to move towards the core are, not dependent on the force-field or program used for MDS analysis [19,20]. When FLD approaches the central core, Bcl-2 and Bcl-2ΔTM become more compact.…”

“…Further, several Caspase-3 cleavage sites are present within the FLD. Phosphorylation and/or caspase-cleavage are important in the activity regulation of Bcl-2 [18,19]. The FLD structure has not been resolved.…”

“…As a consequence, Bcl-2β proteins lacking the TMD reside in the cytoplasm [13]. There is insufficient information regarding the contributions of the TMD region to the overall conformational dynamics and membrane targeting ability of Bcl-2, as most in silico and in vitro studies have been performed with constructs lacking the TMD [19,20].…”

Thermal stability and unfolding pathways of hyperthermophilic and mesophilic periplasmic binding proteins studied by molecular dynamics simulation

“…However, there are no general factors for determining thermostability and it is obvious that different proteins gain their thermostability owing to different combinations of the above factors. To attain a general understanding, many experiments and theoretical researches have concentrated on the folding-unfolding process of various proteins depending on temperature (Day, Paschek, & Garcia, 2010;Grottesi et al, 2002;Ilizaliturri-Flores, Correa-Basurto, Benítez-Cardoza, & Zamorano-Carrillo, 2014;Meharenna & Poulos, 2010;Priyakumar, 2012;Priyakumar, Ramakrishna, Nagarjuna, & Reddy, 2010;Tang & Liu, 2007). However, microscopic structures of proteins and trapping of dynamic intermediates in this process have always been intractable because of the tiny tempo-spatial scales.…”