**3.8 Relative binding affinity of TauR2 towards neuronal specific tubulin isotypes**

The relative binding affinity of TauR2 towards neuronal specific tubulin isotypes (β/α/β) was analyzed by performing MMPBSA calculations for complexes


#### **Table 6.**

*Electrostatic interactions between different* β*/*α*/*β*-tubulin isotypes and TauR2 after molecular dynamics simulations.*

6CVN-tau, 6CVN\*-tau, βI/α/βI-tau, βIIb/α/βIIb-tau and βIII/α/βIII-tau etc. The energy components that govern the binding energy are recorded in **Table 7**. This analysis reveals that, βIII/α/βIII-tau complex shows most favorable interactions while 6CVN-tau complex is least favorable as supported by the binding energy values listed in **Table 7**. Thus, it is interesting to note the significance of C-terminal tail of the tubulin subunits in the stable binding of the tau repeat R2 to stabilize this complex. The order of calculated binding energy in between TauR2 with neuronal specific tubulin-TauR2 complexes is βIII/α/βIII > βIIb/α/βIIb >6CVN\* > βI/α/ βI > 6CVN. The electrostatic interactions in these complexes contribute significantly to the binding energy particularly in βIII/α/βIII-TauR2 and βIIb/α/βIIb-TauR2 complexes when compared to the 6CVN and βI/α/βI tubulin subunits (**Table 7**). The complex βI/α/βI-TauR2 exhibits higher binding energy leading to its weaker affinity towards TauR2. In addition to βIII/α/βIII-TauR2 the complex βIIb/α/βIIb-TauR2 also exhibits relatively higher affinity towards TauR2 compared to rest other complexes. Further, contribution of the individual residues in the binding energy has been investigated by calculating the decomposition energy for each residue. This analysis reveals that, residues from the H12 helix and C-terminal tail of tubulin subunits shows maximum contribution in the binding energy (**Figure 13**). The per-residue

**89**

Binding Energy

**Figure 12.**

*(E)* β*III/*α*/*β*III-TauR2.*

**Table 7.**

*in kcal/Mol.*

*Homology Modeling of Tubulin Isotypes to Investigate MT-Tau Interactions*

interactions energy (residue decomposition energy) calculated for various pairs of interacting residues highlights the importance of the interacting residues. The residues from the H12-helices and C-terminal tail region of complex βIII/α/βIII shows maximum contribution (most negative energy) in the non-bonded contacts leading to the stable and tight binding of the tauR2 to the βIII/α/βIII tubulin subunits.

*The relative binding energy of the tubulin-TauR2 complexes calculated using MMPBSA. All energies are given* 

**System 6CVN 6CVN\*** β**I/**α**/**β**I** β**II/**α**/**β**II** β**III/**α**/**β**III** Vdw −97.25 ± 0.55 −131.17 ± 0.62 −133.38 ± 0.69 −124.36 ± 0.60 −125.24 ± 0.59 Elec −1232.33 ± 3.43 −1534.36 ± 3.12 −1423.07 ± 2.77 −1659.30 ± 4.68 −1768.65 ± 2.77 Polar 413.98 ± 4.73 349.43 ± 4.18 439.27 ± 2.95 433.79 ± 4.13 505.14 ± 2.92 SASA −12.35 ± 0.06 −15.12 ± 0.07 −17.05 ± 0.05 −15.66 ± 0.06 −16.04 ± 0.05

*The secondary structure changes during MD simulation using DSSP for TauR2. Secondary structure changes observed in (A) 6CVN-TauR2 (B) 6CVN\*-TauR2 (C)* β*I/*α*/*β*I-TauR2, (D)* β*IIb/*α*/*β*IIb-TauR2 and* 

−927.87 ± 3.15 −1331.15 ± 3.19 −1134.13 ± 1.13 −1365.2.26 ± 2.26 −1404.7 ± 1.84

*DOI: http://dx.doi.org/10.5772/intechopen.95792*

*Homology Modeling of Tubulin Isotypes to Investigate MT-Tau Interactions DOI: http://dx.doi.org/10.5772/intechopen.95792*

#### **Figure 12.**

*Homology Molecular Modeling - Perspectives and Applications*

6CVN\*

**Systems Electrostatic interactions Distance (Å)** 6CVN-TauR2 D: LYS8:NZ - A: ALA430:O 4.04432


βI/α/βI-TauR2 D: LYS1: N - A: GLU421:OE1 2.86182

βIIb/α/βIIb-TauR2 A: LYS21:NZ - E: GLU434:OE2 4.3529

βIII/α/βIII-TauR2 A: LYS25:NZ - E: GLU434:OE2 2.68494

D: LYS21:NZ - B: SER439:O 4.66847 D: LYS25:NZ - B: GLU434:OE2 4.90999 D: LYS21:NZ - B: GLU434:OE1 5.38615

A: LYS7:NZ - E: GLU415:OE1 4.9846 A: LYS25:NZ - E: GLU441:OE1 5.12197 A: LYS17:NZ - E: ASP424:OD2 5.27557

D: LYS25:NZ - C: GLU412:OE1 4.31321 D: LYS7:NZ - B: GLU415:OE1 4.45715 D: LYS21:NZ - B: GLU434:OE2 4.75044

A: LYS8:NZ - E: ASP396:OD2 5.021

A: LYS25:NZ - E: GLU450:OE2 2.85019 A: LYS1: N - F: ASP417:OD2 2.91844 A: LYS1: N - F: GLU421:OE2 4.28381 A: LYS7:NZ - E: GLU415:OE1 4.31182 A: LYS21:NZ - E: GLU434:OE1 4.48844 A: LYS17:NZ - E: ASP424:OD2 4.70401 G: LYS392:NZ - A: ASP22:OD2 4.95323 A: LYS21:NZ - E: GLU450:OE2 5.37409

6CVN-tau, 6CVN\*-tau, βI/α/βI-tau, βIIb/α/βIIb-tau and βIII/α/βIII-tau etc. The energy components that govern the binding energy are recorded in **Table 7**. This analysis reveals that, βIII/α/βIII-tau complex shows most favorable interactions while 6CVN-tau complex is least favorable as supported by the binding energy values listed in **Table 7**. Thus, it is interesting to note the significance of C-terminal tail of the tubulin subunits in the stable binding of the tau repeat R2 to stabilize this complex. The order of calculated binding energy in between TauR2 with neuronal specific tubulin-TauR2 complexes is βIII/α/βIII > βIIb/α/βIIb >6CVN\* > βI/α/ βI > 6CVN. The electrostatic interactions in these complexes contribute significantly to the binding energy particularly in βIII/α/βIII-TauR2 and βIIb/α/βIIb-TauR2 complexes when compared to the 6CVN and βI/α/βI tubulin subunits (**Table 7**). The complex βI/α/βI-TauR2 exhibits higher binding energy leading to its weaker affinity towards TauR2. In addition to βIII/α/βIII-TauR2 the complex βIIb/α/βIIb-TauR2 also exhibits relatively higher affinity towards TauR2 compared to rest other complexes. Further, contribution of the individual residues in the binding energy has been investigated by calculating the decomposition energy for each residue. This analysis reveals that, residues from the H12 helix and C-terminal tail of tubulin subunits shows maximum contribution in the binding energy (**Figure 13**). The per-residue

*Electrostatic interactions between different* β*/*α*/*β*-tubulin isotypes and TauR2 after molecular dynamics* 

**88**

**Table 6.**

*simulations.*

*The secondary structure changes during MD simulation using DSSP for TauR2. Secondary structure changes observed in (A) 6CVN-TauR2 (B) 6CVN\*-TauR2 (C)* β*I/*α*/*β*I-TauR2, (D)* β*IIb/*α*/*β*IIb-TauR2 and (E)* β*III/*α*/*β*III-TauR2.*


#### **Table 7.**

*The relative binding energy of the tubulin-TauR2 complexes calculated using MMPBSA. All energies are given in kcal/Mol.*

interactions energy (residue decomposition energy) calculated for various pairs of interacting residues highlights the importance of the interacting residues. The residues from the H12-helices and C-terminal tail region of complex βIII/α/βIII shows maximum contribution (most negative energy) in the non-bonded contacts leading to the stable and tight binding of the tauR2 to the βIII/α/βIII tubulin subunits.

**Figure 13.**

*The H12 and C-terminal tail regions show highest energy contribution for the binding of TauR2 in 6CVN\*,*  β*I/*α*/*β*I,* β*IIb/*α*/*β*IIb and* β*III/*α*/*β*III tubulin subunits except in case of 6CVN which does not have C-terminal tail region.*

Hence, relative binding energy calculations further support all other MD simulation results highlighting the tight binding of TauR2 to the βIII/α/βIII tubulin isotype which is predominantly expressed in the neuronal cells and brain.

## **4. Conclusion**

MTs are distributed across all types of cells and play an important role in the cellular functions. Structurally MTs are made up of α/β heterodimeric subunits. Large diversity of α and β-tubulin isotypes exists which are differently expressed in different types of cells, this makes MTs unique from one another in relative proportion of isotypes. The much elevated expression levels of βII and βIII tubulin isotypes about 58% and 25% respectively have been reported to in neuronal cells and brain [35]. The present study extensively uses molecular modeling approaches including homology modeling, MD simulation, binding energy to investigate the binding mode and interaction of neuronal specific tubulin isotypes with TauR2.

Extensive analysis on MD simulation trajectory shows a stable complex formation in between different tubulin isotype and TauR2. The stability of these complexes is mainly mediated by the interactions of H12 helix and C-terminal tail of the α/β tubulin isotypes with TauR2. TauR2 shows differential binding affinity towards various neuronal specific β-tubulin isotypes (βI, βII and βIII) the order of binding affinity is 'βIII> βIIb>βI'. Thus, it is found that TauR2 expresses greater binding affinity with βIII and βIIb tubulin isotypes which are abundantly expressed in neuronal cells and brain. The molecular modeling strategy adopted in this chapter could be potentially used to understand differential binding affinity of other tau repeats such as R1, R3, R4 towards β tubulin isotypes present in other cell lines. The structures for other repeats could be generated using homology modeling and their interactions with neuronal specific tubulin isotypes could also be studied using similar molecular modeling approach.

**91**

**Author details**

Vishwambhar Vishnu Bhandare

Bombay, Mumbai, India

**Acknowledgements**

**Conflict of interest**

Department of Biosciences and Bioengineering, Indian Institute of Technology

© 2021 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium,

\*Address all correspondence to: vishwayogi@gmail.com

provided the original work is properly cited.

*Homology Modeling of Tubulin Isotypes to Investigate MT-Tau Interactions*

lateral sclerosis and other tauopathy linked neurodegenerative disorders.

ture and functions using molecular modeling techniques.

http://creativecommons.org/licenses/by/4.0/

The author declares no conflict of interest.

I believe that the knowledge on precise molecular origin of differential binding affinity of tau with β tubulin isotypes present different cell types will pave the way for developing effective treatments against tau related disorders such as Alzheimers, Amyotrophic

Thus, homology modeling allows us to investigate important biomolecular interactions whose protein structures are not known and/or difficult to get by using biophysical experiments. This, homology modeling, computational tool has made it easier to address various challenging problems in understanding the basic phenomenon's/pathways in modern biology. Also, it has proven wide successful applications in determining the role of proteins in various genetic diseases, hormonal disorder cancers, neurological disorders and other diseases etc. by exploring protein struc-

VVB is thankful to IIT Bombay for Institute postdoctoral fellowship. Author

is also thankful to Prof. Ambarish Kunwar, Department of Biosciences and Bioengineering, IIT Bombay, Mumbai for fruitful discussion and providing necessary computational resources to perform this research work. Author also sincerely thanks Creative Commons license for giving permission to use data from my manuscript my published research article in Scientific Reports (https://doi.org/10.1038/ s41598-019-47249-7). A copy of creative commons license can be found at the link

*DOI: http://dx.doi.org/10.5772/intechopen.95792*

*Homology Modeling of Tubulin Isotypes to Investigate MT-Tau Interactions DOI: http://dx.doi.org/10.5772/intechopen.95792*

I believe that the knowledge on precise molecular origin of differential binding affinity of tau with β tubulin isotypes present different cell types will pave the way for developing effective treatments against tau related disorders such as Alzheimers, Amyotrophic lateral sclerosis and other tauopathy linked neurodegenerative disorders.

Thus, homology modeling allows us to investigate important biomolecular interactions whose protein structures are not known and/or difficult to get by using biophysical experiments. This, homology modeling, computational tool has made it easier to address various challenging problems in understanding the basic phenomenon's/pathways in modern biology. Also, it has proven wide successful applications in determining the role of proteins in various genetic diseases, hormonal disorder cancers, neurological disorders and other diseases etc. by exploring protein structure and functions using molecular modeling techniques.
