Characterization of heterogeneous intermediate ensembles on the guanidinium chloride-induced unfolding pathway of β-lactoglobulin

Abstract

Folding pathway of β-LgA (β-lactoglobulin) evolves through the conformational α→β transition. The α→β transition is a molecular hallmark of various neurodegenerative diseases. Thus, β-LgA may serve as a good model for understanding molecular mechanism of protein aggregation involved in neurodegenerative diseases. Here, we studied the conformational dynamics of β-LgA in 6 M GdmCl at different temperatures using MD simulations. Structural order parameters such as RMSD, R_g, SASA, native contacts (Q), hydrophobic distal-matrix and free-energy landscape (FEL) were used to investigate the conformational transitions. Our results show that GdmCl destabilizes secondary and tertiary structure of β-LgA by weakening the hydrophobic interactions and hydrogen bond network. Multidimensional FEL shows the presence of different unfolding intermediates at 400 K. I1 is long-lived intermediate which has mostly intact native secondary structure, but loose tertiary structure. I2 is structurally compact intermediate formed after the partial loss of secondary structure. The transiently and infrequently buried evolution of W19 shows that intermediate conformational ensembles are structurally heterogeneous. We observed that the intermediate conformations are largely stabilized by non-native H-bonds. The outcome of this work provides the molecular details of intermediates trapped due to non-native interactions that may be regarded as pathogenic conformations involved in neurodegenerative diseases.

Communicated by Ramaswamy H. Sarma

Keywords:

• β-lactoglobulin
• protein unfolding
• MD simulation
• free-energy landscape
• heterogeneous intermediate

Acknowledgements

FA thanks Indian National Science Academy for the award of Senior Scientist Position. Authors sincerely thank SERB for GPU computational Facility.

Disclosure statement

Authors declare there is no conflict of interest.

Additional information

Funding

This work is supported by the Science and Engineering Research Board (SERB), Government of India (Ref. No.: YSS/2015/000228/LS). AP is thankful to SERB, Govt. of India for the award of Young Scientist. Fellowship for PP is supported from DBT Center of Excellence in Bioinformatics, SC&IS, JNU. NKM is thankful to DBT, India, for the fellowship (DBT/2016/JNU/695).