Upload
uloff
View
218
Download
0
Embed Size (px)
Citation preview
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
1/22
Results of Molecular Dynamics Computations of
the Structural and Electrostatic Properties of
Tubulin and Their Consequences for Microtubules
J. A. Tuszynski, T. Luchko, E. J. Carpenter and E. Crawford
Department of Physics
University of Alberta
Edmonton, AB, Canada
T6G 2J1
April 13, 2004
Abstract
We present the results of molecular dynamics computations based on
the atomic resolution structures of tubulin published as 1TUB and 1JFF
in the Protein Data Bank. Values of net charge, spatial charge distri-
bution and Cartesian dipole moment components are obtained for the
tubulin alpha-beta heterodimer. Physical consequences of these results
and subsequent computations are discussed for microtubules in terms of
the effects on test charges, test dipoles, and neighboring microtubules.
Our calculations indicate typical distances over which electrostatic effects
can be felt by biomolecules, ions, and other microtubules. We also demon-
strate the importance of electrostatics in the formation of the microtubule
1
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
2/22
lattice and the tubulin-kinesin binding strength.
Keywords: tubulin, kinesin, molecular dynamics, microtubules, elec-
trostatics
1 Introduction
Microtubules (MTs) are protein filaments of the cytoskeleton with lengths that
vary but commonly reach 5-10m. They are composed of 9 to 16 protofila-
ments when self-assembled in vitro and almost exclusively of 13 protofilaments
in vivo[1]. These protofilaments are strongly bound internally and are connected
via weaker lateral bonds to form a sheet that is wrapped up into a tube in the
nucleation process. These cylindrical protein organelles, found in all eukary-
otes, are critically involved in a variety of cellular processes including motility,
transport and mitosis[2]. Their component protein, tubulin, is composed of two
polypeptides of related sequence, designated and . In addition to - and
-tubulin, many microtubules in cells require the related -tubulin for nucle-
ation. Two other tubulins, designated and , are widespread, although their
roles are still uncertain. The general structure of MTs has been well established
experimentally. A small difference between the - and -monomers of tubulin
allows the existence of at least two lattice types. Moving around the MT in a
left-handed sense, protofilaments of the A lattice have a vertical shift of 4.92
nm upwards relative to their neighbors. In the B lattice this offset is only 0.92
nm because the - and -monomers have switched positions in alternating fila-
ments. This change results in the development of a structural discontinuity in
the B lattice known as a seam.
At the molecular level tubulins roles are highly complex. For example, mi-
crotubules undergo cycles of rapid growth and disassembly in a process known
as dynamic instability that appears to be critical for microtubule function, es-
2
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
3/22
pecially in mitosis. The kinetics of hydrolysis of the GTP bound to -tubulin is
critical for this process by affecting the loss of the so-called lateral cap that stabi-
lizes the microtubule structure[3]. In addition to forming microtubules, tubulin
interacts with a large number of associated proteins. Some of these, such as
tektin, may play structural roles; others, the so-called microtubule-associated
proteins (MAPs) such as tau or MAP2, may stabilize the microtubules, stim-
ulate microtubule assembly and mediate interactions with other proteins. Still
others, such as kinesin and dynein, are motor proteins that move cargoes, e.g.
vesicles, along microtubules[4].
The precise molecular basis of the properties of tubulin is still not well under-
stood, in part because tubulins highly flexible conformation makes it difficult
to crystallize. In a major advance in the field, the three-dimensional structure
of bovine brain tubulin has been determined by electron crystallography by
Nogales et al. in the presence of zinc ions[5, 6]. Once the three-dimensional
structure of a protein has become known it is possible to use affinity modeling
to predict the structures of related forms of the protein with some degree of
accuracy. The crystallographic results were made available through the Protein
Data Bank (PDB) (entries: 1TUB and 1JFF) which allowed us to view the 3D
atomic resolution structure of tubulin. Each tubulin monomer is composed of
more than 400 amino acids and, in spite of their similarity, slight folding differ-
ences can be seen. It is worth stressing that several different versions of both the
- and -monomers exist and are called isotypes[7]. We have applied affinity
modeling techniques to a series of some 290 different tubulins, representing -
and -tubulins from animals, plants, fungi and protists, as well as several -, -
and -tubulins. A summary of this work will be published elsewhere.
3
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
4/22
2 Conformational and electrostatic changes due
to GTP hydrolysis
Tubulin is believed to exist in two conformational states depending on whether
GTP or GDP is found in the E-site. Importantly, when GTP is found in the
E-site tubulins net charge is reduced by one. Furthermore, it is believed that
having GTP in the exchangeable site is necessary for polymerization while GDP
in the exchangeable site contributes to depolymerization[3].
To determine conformational changes due to GTP hydrolysis a series of sim-
ulations were carried out as described in Section 2.1. 10 coordinate sets per
ps where recorded and analyzed for the final 600ps and 300ps of the first and
second equilibrium runs of GTP and GDP tubulin. Common indicators of con-
formational change such as water accessible surface area, radius of gyration and
RMS fluctuations from the crystal structure showed little difference between
the four runs. Average structures were produced and root-mean-square (RMS)
deviations from the crystal structure as well as differences between the aver-
age structures were taken. Similar changes were found among runs with the
same nucleotide as with different nucleotides suggesting no significant confor-
mational changes were found. Though similar protocols have found conforma-
tional changes in proteins before, for example [8], we believe that these results
are likely because the annealing runs were too short to allow a sufficient con-
formational search to occur. Either several longer annealing runs or alternate
computational techniques are required to achieve this.
2.1 Computational methods
Molecular dynamics simulations with CHARMM[9] and the CHARMM27 force
field[10] were performed using the crystal structure file 1JFF as initial condi-
4
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
5/22
tions for the protein structure. Simulated annealing was preformed on structures
containing GTP and GDP in the exchangeable (E) site. Following this, equi-
librium molecular dynamics was preformed to obtain average structures from
which properties were calculated.
In order to use 1JFF as the initial conditions for our simulations it was
necessary to remove the taxol molecule and zinc ion and add several parts of
the amino acid chains that were missing in the crystal structure. Except for the
C-termini, the locations of the missing residues were obtained from the 1TUB
structure. In addition, we have been able to predict with some confidence the
conformations of the C-termini of tubulin since the C-termini of- and -tubulin
were not resolved in the original electron crystallographic reconstruction of the
tubulin molecule due to their flexibility. Our results raise the possibility that the
movements of the C-termini of tubulin may play a major role in kinesin motility
and that they may have some novel, hitherto unsuspected, roles in ion transport
along microtubules especially in the axoplasm of neurons. The C-termini had
been previously added to 1TUB using MolMol[11] and were added to the 1JFF
structure in the same manner as the other missing residues. Residues 1A-2A,
27A-64A, 436A-451A, 1B-3B, and 435B-455B were added individually by root-
mean-square devitation (RMSD) fitting the backbone atoms of five residues
adjacent to the missing segments on either side and pasting the missing residues
into the new structure.
Besides the Mg2+ ion that was part of the crystal structure 4 Na+, 55
K+ and 6 Cl ions were added to the system to maintain electro-neutrality
and an ion concentration consistent with that of cytoplasm. An additional K+
was added for simulations with GTP in the E-site. These ions were placed
at random positions about the fixed protein in a box 105A X 65A X 125A
and equilibrated for 2ns using Langevin dynamics with a friction coefficient of
5
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
6/22
62ps1 and periodic boundary conditions (PBC)[12]. The two systems were
then hydrated by tiling a box of 3000 pre-equilibrated water molecules and
minimized for 400 steps of steepest descent.
Simulated annealing was then performed based the protocol outlined in [8].
Our systems were heated to 500K in 40ps and held there for 10ps and then
cooled to 200K over 120ps using time steps of 2fs and utilizing SHAKE to
maintain rigid bond lengths. The resulting coordinate sets and their subsequent
simulations will be referred to as GTP1 and GDP1. A second coordinate set
for each system (GTP2 and GDP2) was produced by maintaining the system at
500K for an additional 15ps before cooling. All four coordinate sets were then
equilibrated at 300K for 150ps with 1fs time steps without SHAKE.
A total of 2.1ns of production simulation was performed between the four
systems. GTP1 and GDP1 each were simulated for 600ps while GTP2 and
GDP2 were both simulated for 300ps. Coordinate sets were recorded every
0.1ps.
2.2 Electrostatic properties
For self-assembly of MTs to occur individual tubulins must interact via long-
range forces (i.e. electrostatic forces) for attraction and alignment to occur.
Since tubulin is highly charged and, thus, naturally repulsive to other tubulins
the shape of the electric field and how it interacts with its ionic environment is
of great importance.
To estimate an upper bound for the maximum distance over which tubulin
electric fields may have some significant interaction we may look to the critical
concentration of Tu-GTP required for MT growth. While the concentration
depends on such factors as the use of nucleation seed, a minimal estimate of
5mM[13] may be used. Typically, the Tu-GTP critical concentration in vitro
6
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
7/22
must be higher. This corresponds to an average separation between the centers
of mass of 150A or, between surfaces, of roughly 100A. We can consider this the
maximum distance at which tubulin dimers may interact.
For orientation-dependent measurements, such as the dipole moment, we
have RMSD fit the -helix and -sheet portions of the backbone of each co-
ordinate set to 1JFF. Prior to this we have rotated 1JFF structure 26 with
respect to the protofilament axis (x-axis) such that the y-axis is tangential and
the z-axis is inward and perpendicular to the MT surface[14].
Furthermore, unless otherwise noted, all electrostatics calculations have been
carried out with a dielectric constant of 1 corresponding to a vacuous environ-
ment. Since the force field parameters have been optimized for a dielectric con-
stant of 1 and the simulations performed under such conditions, this produces
the most realistic and relevant results for our simulations. Ions are included
where noted (Mg2+ at the N-site is considered part of the protein) and water
is generally included though explicit waters except where noted.
The porcine tubulin sequences of the - and -monomers used have a typ-
ical net charge of -24e each at pH 7.0. Including the two nucleotides and the
bound Mg2+ the net charge of the structure is -53e and -54e for GDP bound
and GTP bound tubulin, respectively. Although we have found no significant
conformational differences between any of our simulations we will report the
electrostatic properties of both GDP bound and GTP bound tubulin separately
due to the differences in net charge.
Although no obvious conformational differences were found between GTP1,2
and GDP1,2 there was a difference in ionic condensation around the exchange-
able site. In both GDP1 and GDP2 a positive ion is tightly bound to the surface
of the exchangeable nucleotide analogous to Mg2+ at the non-exchangeable site.
In GTP1,2 two positive ions are tightly bound to the surface of the nucleotide.
7
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
8/22
Over the length of the runs these bound ions had an average root-mean-square
fluctuation (RMSF) of 0.79A for GTP1,2 and 0.53A for GDP1,2. Also observed
in all simulations was a single ion oscillating 5 to 8A from the exchangeable
nucleotides. Not strongly bound, these had an average RMSF value of 5.7A for
GTP1,2 and 4.3A for GDP1,2.
While several ions in all of the simulations became bound to the surface,
other than around the E-site, only one other site bound ions in all simulations.
A single sodium in GDP1,2 and a single potassium in the case of GTP1,2 was
found between residues 417 and 426 of the -monomer. This is a highly charged
area of the N-terminal end of the H12 helix. The sodium ions found in GDP1,2
were much more tightly bound with RMSF of 1.2A as compared to 5.1A for the
potassium ions in GTP1,2.
The distribution of the electrostatic potential on the surface of the protein
in the absence of water and ions is shown in Figure 1. Due to the large net
charge of tubulin the surface potential is completely negative. However, poten-
tial gradients can be seen across the surface along the lateral and longitudinal
directions that are important for binding within the MT. Laterally the almost
neutral side of the tubulin, Figure 1(f), will be in contact with its negative side,
Figure 1(e), of its neighbors. Similarly, the exposed end of the -monomer, Fig-
ure 1(d) is quite negative in comparison to the exposed end of the -monomer,
Figure 1(c), particularly around the E-site.
[Figure 1 about here.]
The shape of the electric field at large distances is typically discussed in terms
of the multipole expansion. Unfortunately, neither the dipole nor quadrupole
moment can be uniquely defined for a structure that has a non-zero net charge.
However, by using the center-of-mass as our origin we can attempt to quantify
the distribution of charge within the molecule and how this may affect long-range
8
http://-/?-8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
9/22
interactions. How this shape changes with the addition of ions and the multipole
approximation to it can be seen in Figure 2. Table I summarizes the results of
our calculations of the tubulins net charge, dipole moment from our simulations.
Note that the x-direction in Table 1 coincides with the protofilament axis. The
-monomer is in the direction of increasing x values relative to the -monomer.
The y-axis is oriented radially towards the MT center and the z-axis is tangential
to the MT surface.
[Table 1 about here.]
[Figure 2 about here.]
2.3 Dimer-dimer interactions
Protofilament and microtubule dynamics are a result of tubulin dimer-dimer
interactions. In order to quantify these interactions a potential energy map
was produced by moving one tubulin dimer relative to another (see Figure 3)
and calculating the electrostatic and Lennard-Jones interaction energy in the
absence of water and ions using CHARMM and a 30A cut-off.
[Figure 3 about here.]
The mapping of dimer-dimer interactions was done in a planar grid tangent
to the MT surface. The grid spacing used was 2 A with center-of-mass displace-
ments ranging from 0 to 120A longitudinally and -80A to 80A laterally. Due
to the symmetry created by using pairs of identical dimers (produced from the
average structures of GTP1 and GDP1) it was not necessary to perform calcu-
lations with a negative displacement in the longitudinal axis. Rotation of the
dimers was not varied with the lateral separation. As a result these calculations
may more closely represent protofilament sheets than MTs.
9
http://-/?-http://-/?-http://-/?-8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
10/22
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
11/22
steps of 1 fs.
Conformational changes that were found in tubulin have been seen to affect
both lateral and longitudinal contacts, providing some insight into the nature of
the dynamical instability of microtubules. We have also seen that the hydrolysis
state of kinesin affects its binding affinity for tubulin. Figure 4 shows the shape
of the binding potential whose depth is approximately 0.5 eV corresponding
closely to the ATP hydrolysis energy that drives the process of kinesins walk
along the filament. Figure 5 shows the electric charge distribution on the motor
domain of kinesin that appears complementary to the charges on tubulin. Fur-
thermore, the calculated kinesin binding site of MTs agrees with results from
crystallography. (see Figure 6)
[Figure 4 about here.]
[Figure 5 about here.]
[Figure 6 about here.]
4 Conclusions
The electrostatic charge of tubulin, although significantly screened by counter-
ions in solution, could affect microtubule assembly by influencing dimer-dimer
interactions on relatively short distances (approximately 5 nm) and the kinetics
of assembly. This has been recently demonstrated by Sept et al[16] who cal-
culated the electrostatic energy of protofilament-protofilament interactions and
concluded from their work that the two types of microtubule lattices (type A
and B) correspond to the local energy minima.
The dipole moment could play a role in microtubule assembly and other
processes also. This could be instrumental in the docking process of molecules to
tubulin and in the proper steric configuration of a tubulin dimer as it approaches
11
http://-/?-8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
12/22
a microtubule for binding. A tubulin dimer surrounded by water molecules and
counter-ions has a dominant dipolar contribution to the electrostatic energy as
shown in Figure 2. Once a microtubule has been formed, the greater the dipole of
each of its units is, the less stable the microtubule since dipole-dipole interactions
provide a positive energy disfavoring a microtubule structure. Note that the
strength of the interaction potential is proportional to the square of the dipole
moment hence microtubule structures formed from tubulin units with larger
dipole moments should be more prone to undergo disassembly catastrophes
compared to those microtubules that contain low dipole moment tubulins.
In work published elsewhere [17] we have also considered the role of elec-
trostatics in the interactions between tubulin, microtubules and other charged
or polarized molecules. In particular, we have shown that in spite of Debye
screening, a microtubule can exert a Coulomb force on a charged particle that
is up to 5 nm away from its surface. The dipole-dipole forces that have been
calculated are negligible for the most part. However, when two microtubules
are found in the same vicinity, they can exert significant forces of repulsion even
in the presence of ionic screening. This is increased by the negatively charged
C-termini protrude perpendicularly to the microtubule, explaining the existence
of the so-called zone of exclusion[2] known to cell biologists for many years.
We have shown that the microtubule structure, in particular the lateral
binding between protofilaments, is consistent with the location of positive and
negative segments of the electrostatic potential for optimal binding. It is worth
mentioning that a recent paper[18] showed the electrostatic surface of the whole
microtubule following computations involving the Poisson-Boltzmann equation.
From these calculations a dramatic difference between the plus and minus ends
of a microtubule has been revealed. It is very likely that this difference leads to
the well-known difference in polymerization kinetics involving these two ends.
12
http://-/?-8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
13/22
Finally, the state of the C-termini could mediate how motor proteins such as
kinesin bind to and move on microtubules. Our simulations show that kinesin
binds preferentially to upright C-termini and not to C-termini lying on the
surface of the microtubule. Very minor changes in the local ionic environment
or the pH could halt the processive motion of a two-headed kinesin by collapsing
the C-termini. One can postulate that the proportion of C-termini that are in
the upright conformation in a given portion of the microtubule could determine
the actual rate of kinesin movement. It is likely that such arguments could
apply to other motor proteins as well.
We hope that the new insights gained by performing these computations
will be useful in our understanding of the cellular machinery as well as in the
efforts to construct nanomachinery that uses biomolecular components or hybrid
structures mimicking the effects observed in living cells.
Acknowledgments
This research was supported by grants from NSERC and MITACS-MMPD.
References
[1] D. Chretien and R. Wade, Biol. Cell 71, pp. 161174, (1991).
[2] P. Dustin, Microtubules, Springer-Verlag, Berlin, (1984).
[3] H. Flyvbjerg, T. Holy, and S. Leibler, Phys Rev. E. 54(5), pp. 55385560,
(1996).
[4] M. Kikkawa, E. Sablin, Y. Okada, H. Yajima, R. Fletterick, and N. Hi-
rokawa, Nature 411, pp. 439445, (2001).
13
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
14/22
[5] E. Nogales, S. Wolf, and K. Dowling, Nature 391, pp. 199203, (1998).
PDB ID 1TUB.
[6] J. Lowe, H. Li, K. Dowling, and E. Nogales, J. Mol. Biol. 313, pp. 1045
1057, (2001). PDB ID 1JFF.
[7] Q. Lu, G. Moore, C. Walss, and R. Luduena, Structural and functional
properties of tubulin isotypes in Advances in Structural Biology, 5, pp. 203
227, Jai Press, Stanford U.S.A., (1998).
[8] W. Wriggers and K. Schulten, Biophysical Journal 75, pp. 646661, (1998).
[9] B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan,
and M. Karplus, J. Comp. Chem 4, pp. 187217, (1983).
[10] A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. Dunbrack Jr.,
J. Evanseck, M. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-
McCarthy, L. Kuchnir, K. Kuczera, F. Lau, C. Mattos, S. Michnick, T. Ngo,
D. Nguyen, B. Prodhom, W. Reiher, III, B. Roux, M. Schlenkrich, J. Smith,
R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and
M. Karplus, J. Phys. Chem. B 102, pp. 35863616, (1998).
[11] R. Koradi, M. Billeter, and K. Wuthrich, J. Mol. Graphics 14, pp. 5155,
(1996).
[12] B. Roux, Personal communications (2002).
[13] M. Symmons, S. Martin, and P. Bayley, Journal of Cell Science 109,
pp. 27552766, (1996).
[14] H. Li, D. J. DeRosier, W. V. Nicholson, E. Nogales, and K. H. Downing,
Structure 10, pp. 13171328, (2002).
14
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
15/22
[15] V. VanBuren, D. J. Odde, and L. Cassimeris, PNAS 99, pp. 60356040,
(2002).
[16] D. Sept, N. Baker, and J. A. McCammon, Protein Science 12, pp. 2257
2261, (2003).
[17] J. Tuszynski, J. Brown, E. Crawford, E. Carpenter, M. Nip, J. Dixon, and
M. Sataric, Mathematical and Computer Modelling , (accepted April 11
2003).
[18] N. Baker, D. Sept, S. Joseph, M. Holst, and J. McCammon, Proceedings
of the National Academy of Sciences 21, pp. 1003710041, (2001).
[19] W. Humphrey, A. Dalke, and K. Schulten, J. Molecular Graphics 14,
pp. 3338, (1996). http://www.ks.uiuc.edu/Research/vmd/.
15
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
16/22
Results of Molecular Dynamics Computations of the Structural andElectrostatic Properties of Tubulin and Their Consequences for Microtubules
J. A. Tuszynski et al.
(a) (b)
(c) (d)
(e) (f)
Figure 1: Electrostatic potential at the water accessible surface. Blue is neg-ative, white is neutral and red (none shown) is positive. The views are facingradially out of (a) and into (b) the MT, the exposed -end (c) and the exposed-end (d) and tangential to the MT with the monomer on the right(e) andthe left (f). Images created with VMD [19].
16
http://-/?-http://-/?-8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
17/22
Results of Molecular Dynamics Computations of the Structural andElectrostatic Properties of Tubulin and Their Consequences for Microtubules
J. A. Tuszynski et al.
(a) (b) (c)
Figure 2: A tubulin dimer in vacuum (a) is seen principally as a monopole fromthe point of view of the electrostatic potential while it is mainly dipolar when
surrounded by counterions and water ((b) and (c)). Images created with VMD[19].
17
http://-/?-8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
18/22
Results of Molecular Dynamics Computations of the Structural andElectrostatic Properties of Tubulin and Their Consequences for Microtubules
J. A. Tuszynski et al.
(a) (b)
Figure 3: Potential energy tubulin-tubulin interaction map for the average struc-
tures of (a) GTP1 and (b) GDP1. The axes represent the center-of-mass dis-placement between the two dimers while the colour represents the potentialenergy in kcal/mole. Areas of high steric conflict have been colored blue.
18
http://-/?-8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
19/22
Results of Molecular Dynamics Computations of the Structural andElectrostatic Properties of Tubulin and Their Consequences for Microtubules
J. A. Tuszynski et al.
Potential
(eV)
Kinesin Position
Along Protofilament ()
Kinesin
Position
()
Figure 4: Map of the interaction energy between a kinesin head and a protofil-ament.
19
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
20/22
Results of Molecular Dynamics Computations of the Structural andElectrostatic Properties of Tubulin and Their Consequences for Microtubules
J. A. Tuszynski et al.
Figure 5: Electrostatic potential at the water accessible surface of the kinesinhead domain (PDB ID: 1I6I)[4]. Figure prepared using MolMol[11].
20
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
21/22
Results of Molecular Dynamics Computations of the Structural andElectrostatic Properties of Tubulin and Their Consequences for Microtubules
J. A. Tuszynski et al.
Figure 6: A kinesin head domain is shown bound to two tubulin monomers.Data from PDB file 1IA0[4]. Image created with VMD [19].
21
8/3/2019 J.A. Tuszynski, T. Luchko, E.J. Carpenter and E. Crawford: Results of Molecular Dynamics Computations of Structura
22/22
Table I: The key electrostatic properties of the tubulin dimer withGTP or GDP in the exchangeable site.
Tubulin properties Tu-GTP RMSF Tu-GDP RMSF(w.r.t. center of mass)
charge (electrons) -54 -53dipole (Debye)
overall magnitude 4850 360 5090 140x-component 700 140 870 220y-component 200 180 370 410z-component 4800 341 4970 130
22