**3.6 Intermolecular interactions between tubulin and TauR2 in tubulin-TauR2 complexes**

The total number of hydrogen bonds formed between tubulin isotypes and TauR2 during the MD simulations are calculated using in-built *'gmx hbond'* command [46]. The cut-off value for the measurement of H-bond was set to 3.4 Å. Consistent H-bond formation was observed throughout the MD simulation in all tubulin-TauR2 complexes. The average number of H-bonds roughly varies between 10 to 20 as shown in **Figure 11**. The details of atom participating in the hydrogen bonding interactions present between tubulin isotypes and TauR2 in the MD simulation end-structures are listed in **Table 4**. All the hydrophobic interactions participating in the formation of stable tubulin-TauR2 complexes are listed in **Table 5**. The βIII/α/βIII-TauR2 complex shows the maximum number of electrostatic interactions when compared to other tubulin-TauR2 complexes (**Table 6**). Further, to understand the role of TauR2

**83**

using DSSP.

*bound TauR2. Color scheme same as Figure 3.*

**Figure 9.**

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

in stabilizing tubulin subunits, secondary structure analysis on TauR2 was done

*Contact surface area (CSA) and solvent accessible surface area (SASA) of different* β*/*α*/*β*-tubulin subunits andTauR2. (A) CSA for different 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) complexes. (B) hydrophobic SASA for tubulin isotype* 

Tau belongs to the class of intrinsically disordered proteins for which no definitive secondary structure exists. Hence their structure determination is difficult by using existing biophysical techniques like X-ray crystallography and NMR. Previous experimental observations propose that tau repeat undergoes a conformational changes from the disordered to ordered state when it binds to the MT [2, 83–86]. Hence, the secondary structural changes during the MD simulations in the TauR2

**3.7 Conformational changes in TauR2 upon tubulin binding**

*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 9.**

*Homology Molecular Modeling - Perspectives and Applications*

end-structures obtained from trajectory.

**tubulin-TauR2 complexes**

**3.6 Intermolecular interactions between tubulin and TauR2 in** 

The total number of hydrogen bonds formed between tubulin isotypes and TauR2 during the MD simulations are calculated using in-built *'gmx hbond'* command [46]. The cut-off value for the measurement of H-bond was set to 3.4 Å. Consistent H-bond formation was observed throughout the MD simulation in all tubulin-TauR2 complexes. The average number of H-bonds roughly varies between 10 to 20 as shown in **Figure 11**. The details of atom participating in the hydrogen bonding interactions present between tubulin isotypes and TauR2 in the MD simulation end-structures are listed in **Table 4**. All the hydrophobic interactions participating in the formation of stable tubulin-TauR2 complexes are listed in **Table 5**. The βIII/α/βIII-TauR2 complex shows the maximum number of electrostatic interactions when compared to other tubulin-TauR2 complexes (**Table 6**). Further, to understand the role of TauR2

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

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

**82**

**Figure 8.**

*Contact surface area (CSA) and solvent accessible surface area (SASA) of different* β*/*α*/*β*-tubulin subunits andTauR2. (A) CSA for different 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) complexes. (B) hydrophobic SASA for tubulin isotype bound TauR2. Color scheme same as Figure 3.*

in stabilizing tubulin subunits, secondary structure analysis on TauR2 was done using DSSP.

#### **3.7 Conformational changes in TauR2 upon tubulin binding**

Tau belongs to the class of intrinsically disordered proteins for which no definitive secondary structure exists. Hence their structure determination is difficult by using existing biophysical techniques like X-ray crystallography and NMR. Previous experimental observations propose that tau repeat undergoes a conformational changes from the disordered to ordered state when it binds to the MT [2, 83–86]. Hence, the secondary structural changes during the MD simulations in the TauR2

#### **Figure 10.**

*Solvent accessible surface area for different tubulin subunits. SASA plotted for 6CVN (black), 6CVN\* (orange),* β*I/*α*/*β*I (green),* β*IIb/*α*/*β*IIb (cyan),* β*III/*α*/*β*III (violet) are shown.*

**Figure 11.**

*The number of hydrogen bonds formed in between tubulin subunits and TauR2 during MD simulation. Color scheme is same as* **Figure 3***.*

were studied using DSSP [56]. **Figure 12** represents conformational changes in the secondary structure of TauR2 upon binding to the tubulin. TauR2 in 6CVN- TauR2 (**Figure 12A**) and 6CVN\*- TauR2 complexes (**Figure 12B**) show formation of short and transient 310-helix during the simulation. The TauR2 in βI/α/βI- TauR2 complex does not form either α-helix or transient 310-helix as shown in **Figure 12C**. The TauR2 in βIIb/α/βIIb-TauR2 complex shows the formation of short-lived α-helix and

**85**

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

**System Atoms involved in H-bonding Distance (Å) Angle (°)** 6CVN-TauR2 D: SER16: HG - B: GLU434:OE2 1.55968 170.912


βI/α/βI-TauR2 D: SER20: HG - B: GLU434:OE2 1.71015 154.981

C: LYS392:HZ2 - D: ASP22:OD1 1.79981 155.003 D: SER20:H - B: GLU434:OE1 1.80025 149.621 D: CYS18:H - B: ASP431:OD1 1.8071 147.422 D: GLY19:H - B: ASP431:OD1 1.81516 170.051 D: ASN23:HD21 - C: PHE389:O 1.83614 168.422 D: ILE5:H - B: GLU415:OE1 1.87843 148.138 B: ARG402:HH22 - D: LYS7:O 1.95256 131.998 D: LYS21:HZ3 - B:ASP438:O 1.96835 128.744 C: ARG391: HE - D: SER20:O 1.97398 162.451 D: ASN6:H - B: GLU415:OE2 1.97803 165.667 D: LYS17:HZ2 - B: ASP424:OD1 2.01656 167.691

A: ASN6:HD21 - G: GLN433:OE1 1.68122 165.335 A: LYS1:HZ1 - G: ASP417:OD1 1.73491 152.719 A: LYS7:HN - E: ALA400:O 1.75148 168.412 A: SER12: HG - A: ASP10:OD2 1.77457 163.204 E: LYS401:HZ1 - A: ASN6:OD1 1.77792 156.289 A: SER20:HN - E: GLU434:O 1.8254 168.05 A: ILE4:HN - G: GLN424:OE1 1.85744 159.004 F: ARG391:HH21 - A: SER20: OG 1.88141 150.648 A: LYS17:HN - E: ASP431:OD2 1.88237 156.579 A: LYS1:HT2 - G: ASP417:OD2 1.93321 163.221 A: LYS25:HZ2 - A: VAL27: OXT 1.95566 155.991 F: ARG391: HE - A: SER20:O 1.95954 137.171 A: SER12:HN - A: ASP10:OD2 1.97395 166.966 A: VAL2:HN - G: GLU421:OE2 1.97952 167.491 A: SER20: HG - E: TYR262: OH 2.01579 158.876 A: CYS18:HN - E: ASP431:OD2 2.04985 143.832 A:ASP22:HN - A: ASP22:OD1 2.06458 123.428

D: LYS17:H - B: ASP431:OD2 1.73879 154.124 D: SER16: HG - B: ASP431:OD2 1.75545 159.778 D: VAL2:H - A: GLU421:OE1 1.79605 175.632 D: SER20:H - B: GLU434:OE2 1.79906 165.806 D: LYS21:HZ1 - B: GLU434:O 1.82861 143.493 B: LYS430:HZ2 - D: VAL14:O 1.84508 147.656 D: ASN23:HD22 - C: PHE389:O 1.87483 147.025 D: LYS1:H3 - A: ASP417:OD1 1.96013 159.665 D: LYS7:H - B: ALA400:O 2.03926 154.297 D: ILE4:H - A: GLN424:OE1 2.05966 141.181

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

6CVN\*


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

*Homology Molecular Modeling - Perspectives and Applications*

were studied using DSSP [56]. **Figure 12** represents conformational changes in the secondary structure of TauR2 upon binding to the tubulin. TauR2 in 6CVN- TauR2 (**Figure 12A**) and 6CVN\*- TauR2 complexes (**Figure 12B**) show formation of short and transient 310-helix during the simulation. The TauR2 in βI/α/βI- TauR2 complex does not form either α-helix or transient 310-helix as shown in **Figure 12C**. The TauR2 in βIIb/α/βIIb-TauR2 complex shows the formation of short-lived α-helix and

*The number of hydrogen bonds formed in between tubulin subunits and TauR2 during MD simulation. Color* 

*Solvent accessible surface area for different tubulin subunits. SASA plotted for 6CVN (black), 6CVN\** 

*(orange),* β*I/*α*/*β*I (green),* β*IIb/*α*/*β*IIb (cyan),* β*III/*α*/*β*III (violet) are shown.*

**84**

**Figure 11.**

*scheme is same as* **Figure 3***.*

**Figure 10.**


#### **Table 4.**

*Hydrogen bonding interaction between tubulin subunits and TauR2 after molecular dynamics simulations.*


**87**

βIII/α/βIII tubulin subunits.

**isotypes**

**Table 5.**

*simulations.*

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

**System Hydrophobic Interactions Distance (Å)** βI/α/βI-TauR2 B: ALA426 - D: LEU11 4.086

βIIb/α/βIIb-TauR2 E: ALA427 - A: LYS17 3.91294

βIII/α/βIII-TauR2 E: ALA426 - A: LEU11 3.83867

B: ALA426 - D: VAL14 4.25902 A: PHE425 - D: ILE4 4.29071 B: ALA427 - D: VAL14 4.57533 A: PHE260 - D: VAL2 4.62894 B: TYR262 - D: CYS18 4.75533 B:PRO263 - D: LYS17 4.89022 B: ARG402 - D: LYS7 4.99921 D: CYS18 - B: VAL435 5.09522 B: ARG422 - D: LEU9 5.15149 B: LYS430 - D: VAL14 5.38523 A: ALA428 - D: ILE4 5.40848 B: VAL440 - D: LYS21 5.41789 C: ILE405 - D: ILE24 5.46457

E: ALA426 - A: VAL14 3.93471 E: ALA426 - A: LEU11 4.19609 A: CYS18 - E: ARG264 4.36259 E: ALA400 - A: LYS8 4.4046 A: CYS18 - E:PRO263 5.04073 A: CYS18 - E: ILE265 5.21553 G: LYS392 - A: ILE24 5.27213 E: TYR399 - A: LEU9 5.32769

E: ALA426 - A: VAL14 4.14469 E: ALA427 - A: LYS17 4.22472 E: ALA427 - A: VAL14 4.83218 E: ARG422 - A: LEU11 4.84097 A: LYS25 - E: VAL437 5.06163 A: CYS18 - E: ARG264 5.14951 E: ARG422 - A: LEU9 5.48905

310-helix (**Figure 12D**). The terminal residues of TauR2 from Ser293 to Val300 in βIII/α/βIII-TauR2 complex () undergoes turn to α-helix conformational transition (**Figure 12E**). Therefore, it is proposed that this conformational transition of TauR2 from disordered to ordered state promotes the stable binding of TauR2 with the

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

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

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

*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*

**Table 5.**

*Homology Molecular Modeling - Perspectives and Applications*

**System Hydrophobic Interactions Distance (Å)** 6CVN-TauR2 B: ALA427 - D: LYS17 4.23972

*Hydrogen bonding interaction between tubulin subunits and TauR2 after molecular dynamics simulations.*

βIII/α/βIII-TauR2 A: SER16: HG - E: ASP431:OD1 1.57372 172.137

**System Atoms involved in H-bonding Distance (Å) Angle (°)** βIIb/α/βIIb-TauR2 A: SER16: HG - E: ASP431:OD1 1.71023 174.429

> A: LYS17:HZ2 - E: ASP424:OD2 1.72125 162.879 A: LYS1:HT2 - F: GLU421:OE2 1.73767 160.093 A: LYS25:HZ2 - E: GLU445:OE1 1.7524 156.386 A: LYS7:HN - E: ALA400:O 1.7726 158.577 A: ASN6:HD22 - F: ASP431:OD1 1.88399 166.501 A: LYS17:HN - E: ASP431:OD1 1.90489 145.148 E: ARG402:HH12 - A: LYS7:O 1.90591 147.259 A: VAL27:HN - E: GLU445:OE1 1.92907 160.86 A: CYS18:HN - E: ASP431:OD1 2.03765 145.506 A: LYS25:HZ3 - E: GLU446:O 2.04646 165.654 F: GLN424:HE21 - A: LYS1:O 2.06218 173.384

> A: LYS21:HZ1 - E: GLU443:OE2 1.74362 173.969 F: GLN424:HE21 - A: VAL2:O 1.79549 177.625 A: GLN15:HE21 - E: GLU443:OE2 1.81621 154.684 A: LYS8:HZ3 - F: GLU433:OE1 1.84962 164.797 A: LYS8:HZ1 - E: ASP396:OD1 1.85984 168.252 G: ARG391:HH11 - A: ASN23:OD1 1.89423 162.494 E: GLY442:HN - A: ILE24:O 1.93324 171.538 A: LYS17:HN - E: ASP431:OD1 1.99492 142.974 A: CYS18: HG - E: ASP431:OD1 2.0734 155.708


B: ARG264 - D: CYS18 4.32305 B: ALA426 - D: VAL14 4.34456 B: ARG402 - D: ILE4 5.12692 B: VAL409 - D: ILE4 5.16258 B: ARG422 - D: LEU11 5.2126 B: ALA427 - D: VAL14 5.2724

E: ALA426 - A: LEU11 4.1983 E: ALA400 - A: LYS8 4.29681 G: PHE260 - A: ILE4 4.3943 A: VAL2 - G:PRO261 4.85577 A: LEU9 - A: LEU11 5.10635 A: LYS21 - E: VAL437 5.11425 E: ALA427 - A: VAL14 5.28218 A: VAL14 - A: LEU11 5.3507 E: ARG422 - A: LEU9 5.37331 A: VAL2 - A: ILE4 5.42169

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6CVN\*

**Table 4.**

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

310-helix (**Figure 12D**). The terminal residues of TauR2 from Ser293 to Val300 in βIII/α/βIII-TauR2 complex () undergoes turn to α-helix conformational transition (**Figure 12E**). Therefore, it is proposed that this conformational transition of TauR2 from disordered to ordered state promotes the stable binding of TauR2 with the βIII/α/βIII tubulin subunits.
