Comparative insights using the molecular homology model of BDNF (Brain derived neurotrophic factor) of Varanus komodoensis and the known NGF (Nerve growth factor) structure of Naja atra

Abstract

BDNF (Brain derived neurotrophic factor) is a secretion protein and a member of the neurotrophin family of growth factors. Structural and functional characterization of BDNF Varanus komodoensis is of interest while its structure remains unknown. Thus, a homology molecular model of BDNF was constructed for gleaning possible structural insights. The model was compared with the structure of the homologous NGF (Nerve growth factor, another member of neuro-trophin family) from Naja atra. Comparative structural analysis of the models showed structural similarities with their predicted cavities for the interpretation of potential functional analogy.

Background

Brain Derived Neurotrophic Factor (BDNF) function is with development. It accelerates the differentiation of selected neuronal populations of the peripheral and central nervous systems. BDNF participates in axonal growth, path finding and in the modulation of dendritic growth and morphology in many regions of the Central Nervous Systems (CNS). The versatility of BDNF has been proved for its contribution to a range of adaptive neuronal responses including long-term potentiation (LTP), long-term depression (LTD), certain forms of short-term synaptic plasticity, as well as homeostatic regulation of intrinsic neuronal excitability [1]. The Nerve growth factor (NGF) is a protein which stimulates the differentiation and maintenance of sympathetic and embryonic sensory neurons. It is known that snake venoms are a rich source of NGF.

NGF acts as a survival factor in nerve cells and it has metal coordination sites, primarily limited to Zn (II) and Cu (II). It has been found in the brain with highest concentration of metal ions to modulate the function of the nerve cells by efficiently inhibiting the biological activities of NGF. NGF and BDNF are two members of a family of neuro-trophic factors with overlapping molecular function [2]. Three neuro-trophic factors NGF, BDNF, NT3 are highly conserved being the member of the NGF family in vertebrates reflecting molecular conservation during evolution and speciation. It is shown that NT-4protein from Xenopus and Viper has 50-60% amino acid identity with NGF, BDNF, and NT-3 with an extended evolutionary relationship [3]. The study shows that BDNF interacts with TrkB. The involvement of BDNF in glucose metabolism in diabetic and obese mice with sensitivity to the peripheral neurons is shown [4, 5].

Active sites of proteins are characterized with evolving sidechains known as hot spots for protein interactions [6]. BDNF has been considered as an interesting molecule due to its possible association with obsessive compulsive disorder [7], Alzheimer disease [8], and dementia [9]. It should be noted that Varanus and the Naja atra belong to the same family. BDNF is common and it acts as NGF in Varanus komodoensis. However, the structure of BDNF from V. komodoensis is unknown. Therefore, it is of interest to develop its homology model to compare with NGF from Naja atra for establishing similar structural features.

Methodology

Sequence data:

The sequences of BDNF from Varanus komodoensis was downloaded NCBI and that of NGF from Naja atra downloaded from UniPROT (comprehensive, high-quality resource for protein function related information) for this study. The UniPROT database documents predicted function for BDNF from Varanus komodoensis. Hence, it is of inertest to report the homology model [10] for inferring molecular function.

Template selection:

A suitable template (PDB ID: 1BND_A with resolution 2.3 Å) was selected using BlastP (Protein Blast) against the PDB (Protein databank) database for the BDNF query sequence with calculated DOPE Score and molePDF Score (Figure 1).

Figure 1.

DOPE profile of the model with the template is shown as a function of residue position number.

Homology model:

The homology model of BDNF (Figure 2) was developed using Modeller [11] and the model was further analysed for validation using RAMPAGE [12].

Figure 2.

A homology model of BDNF Varanus komodoensis is shown. The homology model [10] was developed using modeler version 9.0 [11].

Cavity prediction and characterization:

The active site prediction server [13] was used for the calculation of cavities. The server outputs data with cavities for PDB (protein databank) input files. The analysis shows 33 cavities in the BDNF homology model and NGF structure Table 1 (see supplementary material). The cavity residue stretch and volume in both BDNF and NGF is shown in (Table 1). The number of residues in the cavity is similar in both BDNF and NGF. However, they differ in their volume. This explains sequence (Figure 3) and structure (Figure 4) level similarity between BDNF and NGF.

Figure 3.

Sequence alignment of Varanus komodoensis BDNF and Naja atra NGF is shown.

Figure 4.

A qualitative visual comparison of NGF from Naja atra and BDNF from Varanus komodoensis is presented.

Discussion

The active site prediction server helped to identify the cavities present in the BDNF protein. 33 cavities are found in the structure with the residue sequence stretch, cavity point and volume cavity to locate the active sites in BDNF for potential ligand binding characterization (Table 1). Cavities in protein surface create physiochemical properties which are required for molecular functions. The sequence alignment between BDNF of NGF is shown in Figure 3 for inferring potential homology [14]. Table 2 (see supplementary material) presents the protein features of BDNF and NGF. Further, analysis shows that BDNF and NGF have 51% sequence level similarity level. The similarity level of BDNF for various vertebrates' species is at 93% and 77% in nucleotide and amino acid sequence, respectively [15]. Reports in Xenopus suggest that leu90 is replaced by a phenylalanine as a result of the transversion of C to T [16]. It has been reported that all isolated sequences contained an extra amino acid residue at position 96 compared to that of NGF [17].

BDNF show three anti parallel B sheets connected to form loops (Figure 4b). BDNF and NGF activate the TrkA and TrkB receptors, respectively and the TrkB receptors have high degree of sequence similarity between them [18]. The interaction of the TrkB receptor with that of BDNF is mediated by multiple contacts. The BDNF structure model demonstrates the presence of lysine 96, arginine 97 and glutamine 84 on its B sheet. This is important for BDNF/ TrkB activity as shown elsewhere [15]. Active sites in enzyme are usually determined by their hydrophobic patches with the involvement of side chains. [16] Active site prediction by its size shows that there are 33 cavities in descending order from 1252 to 162 for BDNF and 1520 to 176 for NGF (Table 1). These predictions have extended the identity of the locations for ligand binding to evaluate the volumetric extent of ligands [17]. It should be noted that the identification and size characterization of some free cavities and the hidden cavities are the initial step for ligand design [18].

The BDNF and NGF (Figure 4a & Figure 4b) show a domain characterised by six conserved cysteine residues [19]. The sequence similarity between BDNF and NGF is shown in Figure 3 at 51%. It has been stated that vertebrate BDNF reached an optimally functional structure very early in the vertebrate evolution [20]. It is observed that BDNF evolution is fragmentary in nature [21, 22] except for Zebra Fish. Thus, the reported homology model of BDNF finds application in understanding its function in relation to its evolutionary molecular conservation.

Conclusion

It is of interest to characterize the structure of BDNF from Varanus komodoensis. Hence, a structural model of the protein was reported with its 33 cavities identified using prediction methods. Comparison of the BDNF homology model with the known NGF structure from Naja atra show structural similarity inferring functional analogy. The model data presented with the predicted cavities finds useful for further in-depth analysis of BDNF from Varanus komodoensis.