**3.4 Compactness of tubulin-TauR2 complexes**

The radius of gyration (*R*g) indicates the level of compactness of the protein system which is helpful in getting an insight into the stability of the protein– protein complex. It also helps to understand folding or unfolding of protein structure during the simulation. The Rg values for all the studied tubulin-TauR2 complex ranges from 38.8–40.5 Å (**Figure 7A**). The complex βIII/α/βIII-TauR2 shows stable Rg value for the entire simulation period however other complexes 6CVN-TauR2 6CVN\*-TauR2, βI/α/βI-TauR2, βIIb/α/βIIb-TauR2 show variations in their Rg values. The absence of C-terminal tail region in the complex 6CVN-TauR2 leads to the less Rg values when compared to other tubulin-TauR2 (**Figure 7A**). **Figure 7B** represents the *R*g values of only TauR2 in different tubulin-TauR2 complexes. The Rg values for TauR2 shows fluctuations between 17.5 to 20 Å in case of 6CVN\*, βIIb/α/βIIb, and βIII/α/βIII complexes except for βI/α/βI complex (**Figure 7B**). The βIII tubulin subunits show *R*g value of ~18 Å and βI tubulin subunits have largest *R*g value of 22.5 Å as shown in **Figure 7B**. On the other hand, TauR2 bound to 6CVN shows uninterrupted decline in *R*<sup>g</sup> values from 21.5 Å to 16.5 Å. This analysis also highlights the importance of C-terminal tail region in the stable binding of tau (**Figure 7B**). It is important to note that βIII tubulin subunits (**Figure 8**) have *R*g values like that of βIII/α/βIII-TauR2 complex (**Figure 7A**). This highlights that the tubulin subunits composed of βIII tubulin isotype are structurally stable after binding to the TauR2. Thus, calculation of Rg values for tubulin-TauR2 complexes, tubulin subunits and TauR2 reveals (i) structural stability of the βIII/α/βIII-tau complex over other complexes and (ii) importance of the C-terminal tail region in the binding of TauR2. Contact surface area (CSA) and solvent accessible surface area (SASA)

**81**

**Figure 7.**

**TauR2 complexes**

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

was calculated using 'gmx sasa' tool of gromacs to understand the exposure of

*Radius of Gyration (Rg) of different tubulin-TauR2 complexes and TauR2. (A) Rg of 6CVN-TauR2 (black), 6CVN\*-TauR2 (orange),* β*I/*α*/*β*I-TauR2 (green),* β*IIb/*α*/*β*IIb-TauR2 (cyan),* β*III/*α*/*β*III-TauR2 (violet) (B) Rg* 

**3.5 Contact surface area (CSA) and solvent accessible surface area for tubulin-**

The CSA and SASA describes the accessibility of a binding interface and protein surface to the solvent, respectively. It is well documented that, TauR2 binds to the MT exterior surface via C-terminal tail region [8, 79–82]. Therefore,

the interface residues of tubulin subunits bound to the TauR2 [46].

*for TauR2 in different tubulin-TauR2 complexes. Color scheme same as* **Figure 3***.*

*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 7.**

*Homology Molecular Modeling - Perspectives and Applications*

plays an important role in the binding of TauR2.

**3.4 Compactness of tubulin-TauR2 complexes**

analysis is discussed in the next section.

values for the tubulin β-subunits in the systems 6CVN\*, βIIb/α/βIIb and βIII/α/ βIII are lesser than those of 6CVN and βI/α/βI tubulin subunits (**Figure 6B**). This observation also highlights the binding of TauR2 at the interdimer interface where residual fluctuations are less. However, the part of C-tail region which has no direct contact with TauR2 is highly flexible (**Figure 6B**). The H12 helix and C-terminal tail region of the tubulin subunits significantly contribute to the noncovalent interactions resulting towards stronger binding of TauR2. Therefore, these intermolecular interactions were analyzed in detail and are discussed in the section '*Intermolecular interactions between tubulin and tau'*. Further, atomic Cα-fluctuations of TauR2 (**Figure 6C**) was also studied for better understanding its conformational behavior during the MD simulations. It is surprising to observe highest fluctuations at the N- and C-terminal region in TauR2 bound to 6CVN, where the C-terminal tail region is absent (**Figure 6C**). Interestingly, residual fluctuations expressed by TauR2 bound to βIII/α/βIII-tau complex are much lesser as compared to 6CVN\*-TauR2, βI/α/βI-TauR2 and βIIb/α/βIIb-TauR2 complexes (**Figure 6C**). This also proves that the C-terminal tail region of tubulin subunits

Overall, RMSF analysis suggests the significance of H12-helix and C-terminal tail region in stabilization of the microtubule by binding of tau repeats (TauR2) and it also reveals the greater affinity of TauR2 towards βIII tubulin isotypes which are overexpressed in neuronal cells and brain. Further compactness of all the tubulin-TauR2 complexes was explored by calculating the radius of gyration (*R*g) and this

The radius of gyration (*R*g) indicates the level of compactness of the protein system which is helpful in getting an insight into the stability of the protein– protein complex. It also helps to understand folding or unfolding of protein structure during the simulation. The Rg values for all the studied tubulin-TauR2 complex ranges from 38.8–40.5 Å (**Figure 7A**). The complex βIII/α/βIII-TauR2 shows stable Rg value for the entire simulation period however other complexes 6CVN-TauR2 6CVN\*-TauR2, βI/α/βI-TauR2, βIIb/α/βIIb-TauR2 show variations in their Rg values. The absence of C-terminal tail region in the complex 6CVN-TauR2 leads to the less Rg values when compared to other tubulin-TauR2 (**Figure 7A**). **Figure 7B** represents the *R*g values of only TauR2 in different tubulin-TauR2 complexes. The Rg values for TauR2 shows fluctuations between 17.5 to 20 Å in case of 6CVN\*, βIIb/α/βIIb, and βIII/α/βIII complexes except for βI/α/βI complex (**Figure 7B**). The βIII tubulin subunits show *R*g value of ~18 Å and βI tubulin subunits have largest *R*g value of 22.5 Å as shown in **Figure 7B**. On the other hand, TauR2 bound to 6CVN shows uninterrupted decline in *R*<sup>g</sup> values from 21.5 Å to 16.5 Å. This analysis also highlights the importance of C-terminal tail region in the stable binding of tau (**Figure 7B**). It is important to note that βIII tubulin subunits (**Figure 8**) have *R*g values like that of βIII/α/βIII-TauR2 complex (**Figure 7A**). This highlights that the tubulin subunits composed of βIII tubulin isotype are structurally stable after binding to the TauR2. Thus, calculation of Rg values for tubulin-TauR2 complexes, tubulin subunits and TauR2 reveals (i) structural stability of the βIII/α/βIII-tau complex over other complexes and (ii) importance of the C-terminal tail region in the binding of TauR2. Contact surface area (CSA) and solvent accessible surface area (SASA)

**80**

*Radius of Gyration (Rg) of different tubulin-TauR2 complexes and TauR2. (A) Rg of 6CVN-TauR2 (black), 6CVN\*-TauR2 (orange),* β*I/*α*/*β*I-TauR2 (green),* β*IIb/*α*/*β*IIb-TauR2 (cyan),* β*III/*α*/*β*III-TauR2 (violet) (B) Rg for TauR2 in different tubulin-TauR2 complexes. Color scheme same as* **Figure 3***.*

was calculated using 'gmx sasa' tool of gromacs to understand the exposure of the interface residues of tubulin subunits bound to the TauR2 [46].

#### **3.5 Contact surface area (CSA) and solvent accessible surface area for tubulin-TauR2 complexes**

The CSA and SASA describes the accessibility of a binding interface and protein surface to the solvent, respectively. It is well documented that, TauR2 binds to the MT exterior surface via C-terminal tail region [8, 79–82]. Therefore,

**Figure 8.** *Radius of Gyration for different tubulin isotypes. Color scheme is same as Figure 3.*

initially contact surface area (CSA) of the interface between the TauR2 and tubulin trimer, was calculated, without considering flexible C-terminal tail region. The CSA of βIII/α/βIII is very less when compared to other tubulin isotypes (**Figure 9A**) this represents the tight binding of TauR2 to the βIII/α/βIII tubulin subunits. The higher CSA for βI/α/βI-TauR2 complex indicates weaker binding of the TauR2 to the βI/α/βI tubulin subunits. Furthermore, least SASA in complex βIII/α/βIII-TauR2 represents tight binding of TauR2 to the βIII/α/βIII (**Figure 9B**). On the other hand, higher hydrophobic SASA of the complex βI/α/ βI-TauR2 indicate the exposure of hydrophobic residues which are responsible for loss of native contacts between tubulin and TauR2. The SASA for 6CVN\*, βI/α/βI, βIIb/α/βIIb, βIII/α/βIII shows higher SASA values between 4900 and 5400 Å when compared to 6CVN-TauR2 (~4500 Å) due to the presence of C-terminal tail region (**Figure 10**). To get detailed understanding of the atomiclevel interaction between tubulin isotypes and TauR2, further hydrogen bonding interactions were estimated during simulation and in the MD simulated end-structures obtained from trajectory.
