Research Article: In silico analysis of the V66M variant of human BDNF in psychiatric disorders: An approach to precision medicine

Date Published: April 18, 2019

Publisher: Public Library of Science

Author(s): Clara Carolina Silva De Oliveira, Gabriel Rodrigues Coutinho Pereira, Jamile Yvis Santos De Alcantara, Deborah Antunes, Ernesto Raul Caffarena, Joelma Freire De Mesquita, Alexandre G. de Brevern.

http://doi.org/10.1371/journal.pone.0215508

Abstract

Brain-derived neurotrophic factor (BDNF) plays an important role in neurogenesis and synapse formation. The V66M is the most prevalent BDNF mutation in humans and impairs the function and distribution of BDNF. This mutation is related to several psychiatric disorders. The pro-region of BDNF, particularly position 66 and its adjacent residues, are determinant for the intracellular sorting and activity-dependent secretion of BDNF. However, it has not yet been fully elucidated. The present study aims to analyze the effects of the V66M mutation on BDNF structure and function. Here, we applied nine algorithms, including SIFT and PolyPhen-2, for functional and stability prediction of the V66M mutation. The complete theoretical model of BNDF was generated by Rosetta and validated by PROCHECK, RAMPAGE, ProSa, QMEAN and Verify-3D algorithms. Structural alignment was performed using TM-align. Phylogenetic analysis was performed using the ConSurf server. Molecular dynamics (MD) simulations were performed and analyzed using the GROMACS 2018.2 package. The V66M mutation was predicted as deleterious by PolyPhen-2 and SIFT in addition to being predicted as destabilizing by I-Mutant. According to SNPeffect, the V66M mutation does not affect protein aggregation, amyloid propensity, and chaperone binding. The complete theoretical structure of BDNF proved to be a reliable model. Phylogenetic analysis indicated that the V66M mutation of BDNF occurs at a non-conserved position of the protein. MD analyses indicated that the V66M mutation does not affect the BDNF flexibility and surface-to-volume ratio, but affects the BDNF essential motions, hydrogen-bonding and secondary structure particularly at its pre and pro-domain, which are crucial for its activity and distribution. Thus, considering that these parameters are determinant for protein interactions and, consequently, protein function; the alterations observed throughout the MD analyses may be related to the functional impairment of BDNF upon V66M mutation, as well as its involvement in psychiatric disorders.

Partial Text

Psychiatric disorders are polygenic and multifactorial brain syndromes [1] characterized by clinically significant behavioral, psychological or biological dysfunction [2]. Psychiatric disorders are considered a major public health problem and are responsible for severe distress and functional impairment in individuals with notorious consequences in those who have been affected and their families and social and work environments [3]. Although the global burden of psychiatric disorders is mainly assigned to the disability and not to the mortality of affected individuals [4], mortality rates in psychiatric patients are much higher than those reported in the general population [5,6]. It is estimated that more than 50% of the population in middle and high-income countries will suffer from at least one psychiatric disorder throughout life. In addition, the estimated cost of these diseases between 2011 and 2030 is thereby projected at US$ 16.3 trillion dollars, which makes the economic cost of psychiatric disorders comparable to that of cardiovascular diseases and higher than that of cancer, diabetes and chronic respiratory diseases [3].

BDNF plays a key role in the proliferation, maturation, and maintenance of neuronal function [8,13]. The most frequent missense mutation of BDNF in humans, V66M [13], is believed to impair protein function and distribution [14,15]. This mutation is associated with the development of psychiatric disorders [13].

Computational (in silico) approaches are efficient and necessary to predict protein structures and study disease-associated mutations. This work provided an accurate and complete model of BDNF in silico. Stability and functional predictions pointed to the low accuracy of the algorithms used in predicting the known deleterious potential of the V66M mutation and showed the importance of combining more than one method to predict the effects of non-synonymous mutations. Phylogenetic analysis indicated that position 66 of BDNF is not conserved; however, it is fundamental for the intracellular sorting and activity-dependent secretion of the protein. The conservation degree of position 66 of BDNF could also be related to the low accuracy of the algorithms used in predicting the known deleterious potential of the V66M mutation, since most of them are based on evolutionary information to make predictions. Furthermore, MD analyses indicated that the V66M mutation does not affect the BDNF flexibility and surface-to-volume ratio, but affects the BDNF essential motions, hydrogen-bonding and secondary structure formation, particularly at its N-terminus. Thus, considering that these parameters are determinant for protein interactions and, consequently, protein function; the alterations observed during the MD analyses may be related to the functional impairment of BDNF upon V66M mutation, as well as its involvement in psychiatric disorders. Especially because the BDNF N-terminus, which contains its pre and pro-region, is crucial for its activity and distribution.

 

Source:

http://doi.org/10.1371/journal.pone.0215508

 

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