Length-dependent stability of α-helical peptide upon adsorption to single-walled carbon nanotube

Length-dependent Stability of a-Helical Peptide Upon Adsorption toSingle-Walled Carbon Nanotube

Kanagasabai Balamurugan, Venkatesan SubramanianChemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600 020, India

Received 27 April 2012; revised 19 September 2012; accepted 8 November 2012

Published online 22 November 2012 in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/bip.22185

This article was originally published online as an accepted

preprint. The ‘‘Published Online’’ date corresponds to the preprint

version. You can request a copy of the preprint by emailing the

Biopolymers editorial office at [email protected]

INTRODUCTION

Studies on the interaction of carbon and other nano-

structures with biological macromolecules have

received wide-spread attention due to their potential

applications as molecular sensors, drug delivery

vehicles, and molecular channels, etc.1–4 Specifically,

single-walled carbon nanotubes (CNTs) have been touted to

be one of the most promising materials owing to their

above-mentioned applications. Thus several experimental

studies have been carried out to understand the interactions

of biological molecules with CNTs.5–8 It is found from

previous studies that the a-helical content of the protein

decreases upon its interaction with the CNT and metal

nanoparticles.9–11 The interaction of amphiphilic a-helical

peptide with CNT has been probed using MD simulation

studies which primarily aims at the separation of CNT bun-

dles using biological functionalization.12,13 Since the function

of the proteins primarily depends on their structures, the

Length-dependent Stability of a-Helical Peptide Upon Adsorption toSingle-Walled Carbon Nanotube

Additional Supporting Information may be found in the online version of this

article.Correspondence to: Venkatesan Subramanian; e-mail: [email protected] or

[email protected]

ABSTRACT:

Earlier studies have shown that the helical content of a-

helical peptide decreases upon its interaction with carbon

nanotube (CNT). Further, the length of the a-helix varies

from few residues in the small globular protein to several

number of residues in structural and membrane proteins.

In structural and membrane proteins, helices are widely

present as the supercoil i.e., helical bundles. Thus, in this

study, the length-dependent interaction pattern of a-

helical peptides with CNT and the stability of isolated a-

helical fragment versus supercoiled helical bundle upon

interaction with CNT have been investigated using

classical molecular dynamics (MD) simulation. Results

reveal that the disruption in the helical motif on

interaction with CNT is directly proportional to the

length of the helix. Also it is found that the shorter helix

does not undergo noticeable changes in the helicity upon

adsorption with CNT. On the other hand, helicity of

longer peptides is considerably affected by its interaction

with CNT. In contrast to the known fact that the stability

of the helix increases with its length, the disruption in the

helical peptide increases with its length upon its

interaction with CNT. Comparison of results shows that

structural changes in the isolated helical fragment are

higher than that in supercoiled helix. In fact, helical

chain in supercoiled bundle does not undergo significant

changes in the helicity upon interaction with CNT. Both

the length of the helical peptide and the inherent stability

of the helical unit in the supercoiled helix influence the

interaction pattern with the CNT. # 2012 Wiley

Periodicals, Inc. Biopolymers 99: 357–369, 2013.

Keywords: helix; CNT; stability; supercoil; molecular

dynamics

Contract grant sponsor: Board of Research in Nuclear sciences (BRNS Sanction),

Mumbai, India

Contract grant number: 2011/37C/56/BRNS/2693

Contract grant sponsor: Council of Scientific and Industrial Research (CSIR), New

Delhi, IndiaVVC 2012 Wiley Periodicals, Inc.

Biopolymers Volume 99 / Number 6 357

decrease in the helical content upon interaction with the

CNTs would affect the function. Recently, we have made

attempts to probe the molecular level interaction responsible

for the decrease in the a-helical content of proteins upon

interaction with nanomaterials.14,15 In addition, the role of

curvature (planarity) of carbon nanomaterials has also been

addressed.16 It is evident from the molecular dynamics simu-

lation that the surface of nanomaterials is primarily

responsible for the disruption in the helical content of the

proteins. It is found that planar graphene sheet significantly

disrupts the helical structure when compared to CNTs. A

very recent study on the interaction of villin head piece

domain protein with the carbon nanotubes and graphene

sheets has also revealed that the helical content is mainly

disrupted by the nanomaterials when compared to other

secondary elements.17 The severity of the planar graphene in

affecting the helical content is also shown in that study.

Analysis of literature on the helical structures in globular

proteins reveals the following information: (i) the most stable

helices are longer than 15 residues, (ii) the average length of

helix is 12 residues and the most commonly occurring helix

has six residues, and (iii) it is found that the secondary struc-

tural element is 100% helical up to the denaturation temper-

ature of the protein.18–22 Both experimental and theoretical

studies have been carried out to understand the relationship

between the length of the a-helix and its stability.23–27 Obser-

vations from these studies confirm that the stability of the

helices increases with increase in its length. It is found from

previous experimental investigation that the average helicity

of a (Ala)12 peptide is 20% whereas the same for (Ala)37 is

86%.27 Earlier theoretical studies have shown that at least 10

residues are necessary to form a stable helix and the average

helicity of the peptide remains almost constant from 10 up

to 40 residues.26 It is also observed in general that the longer

helices are present predominantly in the structural proteins

and membrane proteins whereas in the case of enzymes

which are functional proteins the average helix length is 12

residues. It is clear from the above-mentioned points that the

stability of the helix depends on its length, and the length of

the helix varies from one protein to other. It is also worthy to

mention that the longer helices in the structural and mem-

brane proteins are present in supercoiled form (as helical

bundles), i.e., two or more helices intertwined together. As

numerous previous studies and our own studies have shown

the usefulness of polyalanine (PA) peptides as model for heli-

cal peptides,14-15,26 the PA based helices have been taken as

the model systems. Recently, Grigoryan et al. have used com-

putational approaches to design virus-like protein assemblies

on CNT.28 They have highlighted the principles for organiz-

ing geometrically specific superstructures on the CNT

surface. These organized structures have also been used to

create richly textured multilayered assemblies. In that study,

they have also shown the usefulness of Ca methylene of Gly

or the Cb of Ala containing peptides in a repeating manner

on an a-helix as the elementary structural unit for design of

peptides that form rich structures on the CNT. Further these

authors have illustrated that coiled coil helix (antiparallel

hexamer) containing Gly and Ala residues favorably interact

with the surface of CNT. This virus like peptide coated

CNT surface has also been employed to create assembly gold

nanoparticles into helical arrays along the CNT axis.28

Various PAn (where n is the number of residues and n 5

10, 20, 30, and 40) peptides were chosen as the model

systems to investigate the effect of length-dependent interac-

tion pattern with CNT. These peptides are designated as

PA10, PA20, PA30, and PA40. To understand the difference

between the stability of isolated helix and supercoiled helical

bundle, the interaction of supercoiled helical bundle (with

four a-helices) from soluble N-ethylmaleimide-sensitive

factor attachment protein receptor (SNARE) protein was

selected. To unravel the interaction pattern of isolated chain

with CNT, one of the constituent helical chains (Chain_H)

from the same protein was also chosen for further

investigation.

In this investigation, the following important points have

been addressed using classical molecular dynamic simulation

method:

1. Determining the length-dependent interaction of

a-helix with the CNT.

2. Unraveling interaction pattern of supercoiled helix

with CNT.

Understanding of these points would definitely aid to gain

insight into the nature of interaction of carbon nanomate-

rails with the proteins and associated structural changes.

COMPUTATIONAL DETAILS

Construction of ModelsCarbon Nanotube. Two CNTs of different lengths (�89.6

and 130.7 A) with same chirality (6, 6) were built using

VMD Package (http://www.ks.uiuc.edu/Research/vmd/)29

and used for simulation with PAn systems and SNARE

systems, respectively. To simulate an infinite CNT, a segment

with length equal to the Lz box dimension was aligned along

the z-axis with the terminal carbons sharing a chemical bond

as described in previous investigations.14 As reported in the

earlier study, the carbon atoms of CNT were modeled

358 Balamurugan and Subramanian

Biopolymers

as uncharged Lennard-Jones particles using sp2 carbon

parameters of the ff03 force field.30 Recent study on the inter-

action of nucleic acids with CNT using various force fields

and dispersion corrected DFT calculations have also shown

that the polarizability of the CNTs does not affect the interac-

tion process and the results obtained from the partial charge

models are reliable and computationally much efficient.31

PA Peptides. The PA10, PA20, PA30, and PA40 with their ends

capped by acetyl (ACE) and N-methylamine (NMe) groups

were built in a-helix conformation using PyMol.32 The initial

peptide conformation was taken as perfect a-helix with

backbone dihedral angles of u 5 257.08 and w 5 247.08.

SNARE. It is a membrane protein predominantly composed

of a-helices (�75%). The initial geometry of the protein was

taken from the crystal structure of the neuronal SNARE

complex with 2.4 A resolution (PDB ID 1SFC).33 The coordi-

nates of single helical Chain (Chain_H) and the helical

bundle (Supercoil: Chain_E, Chain_F, Chain_G, and

Chain_H) were taken to study the interaction with CNT.

Models. Different CNT-peptide model systems considered in

this study are denoted as: (i) CNT-PA10, (ii) CNT-PA20, (iii)

CNT-PA30, (iv) CNT-PA40, (v) CNT-Chain_H (isolated helix

from SNARE), and (vi) CNT-Supercoil (helical bundle of

SNARE protein). It is found from our previous study that

ff03 parameters are suitable to probe the interaction of CNT

with a-helical peptide and results are qualitatively similar to

those obtained from simulations using the OPLS-AA force

field.14 On similar lines, Hegefeld et al. have shown that the

ff03 and OPLS-AA results are in best agreement with the

experimental values.34 Based on aforementioned salient

findings, Amber ff03 parameters were employed in this

study.35 In models (i) to (iv), the centre of mass of the

peptide was initially placed at 8.5 A away from the side wall

of CNT and PA peptide was aligned parallel to the length of

the CNT as described in the previous study.14 In the case of

CNT-PA peptide interaction, the results are independent of

the initial geometry of the system which was earlier shown in

our study.14 Based on this finding, initial arrangement of the

peptide was kept parallel to the long axis of the CNT in all

the cases.

Simulation Details

All the systems were solvated with SPC water.36 The box sizes

and number of water molecules present in the various

systems were given in the Table I. MD simulations were

performed using the GROMACS 4.5.3 package (http://

www.gromacs.org/).37–39 Both van der Waals and CH-pinteractions play an important role in the interaction of PA

with CNT. These interactions were parameterized within the

van der Waals parameters of each atom type in the force

fields. It is found from the recent study that the qualitative

description of CH-p interaction is feasible with the help of

ff03 force fields.40 These evidences clearly show that the

above-mentioned force field is suitable for modeling the

CNT-helical peptide systems.

Periodic boundary conditions were applied in three

dimensions to carry out MD simulations in the isothermal-

isobaric (NPT) ensemble. The pressure was controlled at 1

atm and the temperature was retained at 300 K using Parri-

nello-Rahman Barostat and velocity rescaling (V-rescale)

Table I Details of Various Systems Simulated in this Study

System Name Description Box Dimension

No.

Ions

No. Water

Molecules

Time

Simulated

(ns)

CNT-PA10 PA10 was aligned parallel to CNT at about 8.5A

distance from the CNT surface.

6.0 3 6.0 3 9.1 Nil 10,481 20

CNT-PA20 PA20 was aligned parallel to CNT at about 8.5 A


6.0 3 6.0 3 9.1 Nil 10,438 20



6.0 3 6.0 3 9.1 Nil 10,394 20



6.0 3 6.0 3 9.1 Nil 10,365 20

CNT-Chain_H Helical fragment Chain_H of the SNARE protein

alone is taken and aligned parallel to CNT

at about 15 A distance from the CNT surface

7.0 3 7.0 3 13.21 3 Na 20,349 25

CNT-Supercoil Supercoiled four helical bundle of the protein

SNARE is taken and aligned parallel to CNT at

about 15 A distance to Chain_H of SNARE.

8.0 3 8.0 3 13.21 14 Na 25,825 25

Length-Dependent Stability of a-Helical Peptide 359

Biopolymers

thermostat, respectively.41–43 Bonds between hydrogen and

heavy atoms were constrained at their equilibrium length

using the LINCS algorithm.44 Thus 2 fs time step was used to

integrate the equation of motion. Electrostatic interaction

was calculated using Particle Mesh Ewald sum with a non-

bonded cutoff of 10 A.45 The position of CNT atoms were

constrained with a harmonic potential of 1000 kJ/mol/nm2.

The following steps were used for the simulation of model

systems: (i) minimization of the whole system, (ii) solvent

equilibration by restraining both CNT and peptide for 250ps,

and (iii) the equilibration of the whole system for 300ps. The

analysis of the energy parameters revealed that all the systems

were found to be well equilibrated. Then production run of

20 ns was performed for all the systems. The trajectories

were saved at 1 ps interval for further analysis. The analysis

of the trajectories was made using the GROMACS suite of

programs.35–37 The results were visualized using VMD

package.46 Various parameters derived from the simulations

are described in the following section.

ANALYSIS

Root Mean Square Deviation (RMSD)

RMSD of the peptides was calculated with respect to initial

conformation as a function of time using Eq. (1).

RMSD ðtÞ ¼ 1

N

XN

i¼1

kriðtÞ2rið0Þk2

" #1=2

ð1Þ

where ri(t) represents the position of atom i at time t and

the same is compared with ri(0) position of the atom at time

0 and N is the total number of back bone atoms.

Secondary Structure Analysis

The secondary structure analysis of the peptide was per-

formed using the Dictionary of protein secondary structure:

pattern recognition of hydrogen-bonded and geometrical

features protocol (DSSP) available in the do_dssp module of

Gromacs package.47 In this protocol, hydrogen-bonding and

other geometrical parameters were used to assign the second-

ary structures of the peptide.

Helical Fraction

Apart from the terminal ACE and NMe residues, only N-2

residues are in the a-helical conformation in PAn (where n 5

10, 20, 30, and 40) peptides. These residues were considered

for the analysis. The helical fraction of the PA peptide was

calculated by using the following Eq. (2),

HelicalFraction

¼ number of residues in a�helical conformation in PAn

n� 2ð2Þ

Hydrogen Bond Analysis

Hydrogen bonding interactions in a-helical conformation

were calculated from the Eq. (3),

Hi ¼f 1; ððdðHi :::OiÞ � 3:5 AÞ and

ð120� � angle ðOi:::Hi � NiÞ � 180�ÞÞ0; Otherwise

ð3Þ

where Hi is the possible ith intramolecular hydrogen bond

in the alpha helix. The number of hydrogen bonds present

in the a-helix as function of time was calculated from the

trajectory.

Contact Area

The area of the molecular surface buried in contact between

the two macromolecules is called as the interface area or

contact area of the molecular assembly. It was calculated as

Contact area ¼ 1

2ððSASpep þ SASCNTÞ � SAS complexÞ ð4Þ

where SASpep and SASCNT are solvent accessible surface

area of the isolated peptide and CNT, respectively and

SAScomplex is that of the whole assembly of the CNT and

peptide.

RESULTS AND DISCUSSION

Length-Dependent Stability of a-Helix with CNT

The initial and final snapshots of the simulated CNT-PAn

(n 5 10–40) systems are presented in Figure 1. Visual inspec-

tion of the results shows that the structure of PA10 rearranges

significantly during dynamics so that it can favorably interact

with CNT without losing its helicity. On the other hand, dis-

ruptions in the helical structure are observed in the terminal

residues of PA20 upon interaction with CNT. In CNT-PA30

and CNT-PA40 systems, appreciable changes in the helicity of

the peptides have been observed.

The calculated helical fractions of various CNT-PAn (n 5

10, 20, 30, and 40) are displayed in Figure 2. Careful scrutiny

of the results shows that the helical content of PA10 decreases

during the period from 2 to 3 ns and also at 14 ns upon on

interaction with CNT. After 14 ns, its helicity increases to the

maximum possible value. It is worth mentioning that the

f


Biopolymers

PA10 peptide consistently withholds the threshold helicity

value of 1 during most part of the simulation time which is

not observed in the other cases. It can be noted that PA10

regains its helicity after interaction with the CNT. Initial

changes in the helicity facilitate the formation of stable com-

plex between CNT and PA10. The structural snapshot of the

PA10 organization towards the CNT during the simulation is

presented in Supporting Information Figure SI. After forma-

tion of stable complex, the helicity of the PA10 increases. A

similar observation has been observed in the case of interac-

FIGURE 1 Representative structures of the initial and final configurations of different CNT-PAn

(n 5 10, 20, 30, and 40) systems from the MD simulations (water molecules are removed for the

clarity purpose).


Biopolymers

tion of PA20 with CNT. However, the extent of increase in the

helicity after interaction with CNT is significantly less than

that of PA10. Results obtained from MD simulations on

CNT-PA30 and CNT-PA40 show that considerable decrease in

the helical content of these peptides upon interaction with

CNT.

To understand the changes in the helical content of the

chosen model peptides, the number of H-bonds present in

the peptides during simulation has been calculated. Figure 3

illustrates the changes in the H-bonding in PAn systems dur-

ing interaction with CNT. It can be found that the there is an

appreciable fluctuations in the number of H-bonds present

in these helical peptides. In the case of PA10 peptide, a maxi-

mum of eight H-bonds (even nine H-bonds) are observed

through out the simulation which indicates that there is no

significant change in the helical content. In the other pep-

tides models, the number of H-bonds decreases with respect

to time, which shows the loss of backbone H-bonds during

the simulation. Consequently, the helicity of these peptides

decreases on interaction with CNT.

To affirm further about the reduction in the helicity of the

peptides, conformational analysis was carried out using

DSSP protocol. The residue-wise changes in the helical

content of the peptides are depicted in Figure 4. It can be

noted that CNT causes appreciable conformational changes

in the helices (except PA10) in accordance with previous

experimental and theoretical reports.14,15 However, primary

objective of the present study is to gain insight into the effect

of length of the helical peptides and their interaction propen-

sity with CNT.

It is observed from the results that there is a slight disrup-

tion in the helical content of PA10 peptide and it is mostly

populated as a helix. In fact, it is possible to note that a-helix

reorganizes to 310 helix during later part of the simulation.

The occurrence of 310 helix may be attributed to the follow-

ing reasons: (i) shorter helices (around eight residues) are

more stable as 310 helix rather than a a-helix48 and (ii) the

310 helices are more elongated when compared to that of

ideal a-helix. There are three residues per turn in a 310-helix

with 2 A rise per residue in contrast to 4 residues per turn

with 1.5 A rise per residue in an a-helix. Thus marginal

increase in the length of the 310-helix in PA10 facilitates

its interaction with CNT when compared with the same in

a-helical conformation.

It can be seen from Figure 4 that PA20 is longer than PA10

and it losses part of its helicity at its terminals. The induction

of helix to coil transition in PA20 aids its interaction with

CNT. It is interesting to note that both PA30 and PA40

FIGURE 2 Helical fraction of the CNT-PAn (n 5 10, 20, 30, and 40) systems as a function of

time.


Biopolymers

peptides undergo significant changes in the helicity on

interaction with CNT. As a result, the entire length of these

peptides is divided into shorter helical fragments. Overall

DSSP analysis reveals that the extent of disruption caused by

the CNT on the a-helical motif is directly related to the

length of the helix, i.e., longer the helix higher the loss in

helicity.

The variation of RMSD with time of PAn peptides are

depicted in Figure 5. In all the model systems, the fluctuation

in RMSD value attains minimum value after certain time

interval. This observation indicates that the peptides do not

undergo any other structural rearrangement or movement

upon forming stable complex. However, the variation in

RMSD value with time varies from one model to other. In

PA10 and PA20 systems, the range of RMSD is 0.1 to 0.2 nm.

The same range for the PA30 and PA40 is 0.3 to 0.5 nm. It is

understandable from the various results reported in the pre-

vious sections that both PA10 and PA20 undergo marginal

changes in the conformation in accordance with the fluctua-

tion pattern in the RMSD values. On the other hand, CNT

induces significant changes in the PA30 and PA40 peptides

which is reflected in the corresponding variation of RMSD

value with time.

The complex formation between the CNT and the PA

peptide is driven by the hydrophobic interaction as the hydro-

phobicity of both these systems is well known. The hydropho-

bic nature of the interaction between the two systems can be

quantified by calculating the contact area. Thus an attempt

was made to calculate the contact area between CNT and PAn

system. The calculated contact area is given Figure 6. It is

found that the contact area between the system increases rap-

idly during the initial phase of simulation. The saturation of

the contact area fluctuation takes place after formation of

stable complex. It is worthy to mention that the contact area

formed by the smaller peptide (PA10 or PA20) is considerably

less than that of longer peptide (PA30 or PA40). Close analysis

of these results elicits that longer peptide has more surface

area to interact with the CNT. In addition, induction of helix

to coil transition further enhances the length of the peptides

which in turn increases contact area.

The energetic origin of interaction between the two

systems is presented in this section. Both van der Waals

interaction between CNT and PA peptide and electrostatic

interaction of PA peptide were obtained from the MD simu-

lation. Results are plotted in Figure 7. It can be seen that the

van der Waals interaction increases from beginning to the

FIGURE 3 Number of H-bonds present in the CNT- PAn (n 5 10, 20, 30, and 40) systems during

the simulation time.


Biopolymers

end of the simulation. With increase in the length of the pep-

tide, the van der Waals interaction facilitates the interaction

between CNT and peptide. There are no significant variations

in the fluctuation of electrostatic energy of the PA10 peptide

upon interaction with CNT. In the case of PA20, marginal

changes in the fluctuation of electrostatic energy are

observed. The variation of electrostatic energy of PA30 and

PA40 reveals the appreciable reduction in the electrostatic

contribution. Thus, as the length of the peptide increases the

van der Waals interaction between the two systems favors the

formation of CNT-peptide complex whereas the electrostatic

stability of the peptide decreases with increase in the length

of the PA peptide. The decrease in the electrostatic contribu-

tion of longer peptides can be attributed to the reduction in

the H-bonding interaction upon formation of CNT-peptide

complex and associated changes in the helical content.

Interaction of a-Helix and a-Helical Supercoil

with CNT

The initial and final snapshots obtained from the MD

simulations of CNT-Chain_H and CNT-Supercoil systems

are displayed in Figure 8. It is found from the results that the

FIGURE 4 Secondary structure assignment of the CNT-PAn systems as a function of time for the

simulations. (A) CNT-PA10; (B) CNT-PA20; (C) CNT-PA30, and (D) CNT-PA40.


Biopolymers

FIGURE 5 Root mean square deviation (RMSD) of the CNT-PAn

systems with respect to their initial structures. FIGURE 6 Contact area between the CNT-PAn systems as a func-

tion of time.

FIGURE 7 van der Waals interaction between CNT-PAn system and electrostatic interaction

within PAn during the simulation time. (A) CNT-PA10; (B) CNT-PA20; (C) CNT-PA30; and (D)

CNT-PA40.

isolated helix undergoes drastic conformational changes

during dynamics. On the other hand, the structure of super-

coiled helix is retained upon interaction with CNT. It can be

seen from the snapshots that the structural integrity of super-

coiled helix is maintained. To facilitate the interaction, the

supercoiled bundle slides on the surface of CNT.

The helical fraction of the Chain_H on interaction with

CNT in CNT-Chain_H and CNT-Supercoil systems were

calculated. The calculated changes in the helical fraction is

presented in Figure 9. It is observed from the results that the

helicity of isolated helix (CNT-Chain_H) decreases

drastically whereas helicity of individual chains of super-

coiled helix (CNT-Supercoil the Chain_H) is not affected

upon on interaction.

The secondary structure plots of the Chain_H

(CNT-Chain_H) and Chain_H (CNT-Supercoil) are shown

in Figure 10. It can be observed that the isolated helical

peptide undergoes conformational transition from helix to

turns during the simulation. On the other hand, such

changes are not observed in the supercoiled helix on inter-

action with CNT. The overall secondary structural patterns

of all the four chains of the CNT-Superhelix system are

given in Supporting Information Figure SII. Results show

that all the four helices present in the supercoil are stable

and their native structures are preserved upon interaction

with CNT.

The van der Waals interaction energy between the

peptide and the CNT was calculated for CNT-Chain_H and

CNT-Supercoil systems to gain insight into the energetics of

interaction. These results are plotted in Figure 11. It can be

found that the interaction energy of CNT-Supercoil system

is more favorable compared with the CNT-Chain_H model.

On the other hand, the helix present in the supercoil is

structurally stable whereas the same helix in the isolated

condition (helix Chain_H) is disrupted. To understand

further, the interaction energy of the CNT with the protein

FIGURE 8 Representative structures of the initial and final con-

figurations of CNT-Chain_H and CNT-Supercoiled systems from

the MD simulations (water molecules are removed for the clarity

purpose).

FIGURE 9 Helical fraction of the CNT-Chain_H and CNT-

Supercoiled systems as a function of time.


Biopolymers

and the interaction energy of the protein with itself in the

two systems were calculated. The changes in the energetics

are presented in Figure 12. It can be noted that fluctuation

in the interaction energy of the Chain_H with the CNT is

about �100 kcal/mol. The same fluctuation for supercoiled

helix with CNT is almost similar. The variation in the calcu-

lated intramolecular energy of the isolated chain is centered

about �21300.0 kcal/mol. The same energy for the super-

coiled helix fluctuates about �5500.0 kcal/mol. Therefore,

the stability of the supercoiled helix is significantly higher

(fourfold higher) than that of isolated chain. As a conse-

quence, isolated chain undergoes significant conformational

changes upon interaction with CNT compared to that of

supercoiled helix with CNT. These findings clearly reveal

that the length and the inherent stability of the helical

peptide determine the extent of interaction between CNT

and helical fragments.

FIGURE 10 Secondary structure assignment of the (A) CNT-Chain_H and (B) CNT-Supercoil

systems as a function of time.

FIGURE 11 van der Waals interaction energy between CNT and

peptide in the CNT-Chain_H and CNT-Supercoil system as a func-

tion of simulation time.


Biopolymers

CONCLUSIONSIn this study, the interaction pattern of CNT with a-helical

peptides of different lengths (number of residues) has been

probed. In general, it has been shown with the help of both

experimental and theoretical studies that the stability of the

a-helix increases when the length of the helix increases. In

stark contrast to the above-mentioned observation, the

shorter helical peptides are structurally more stable on inter-

action with CNT whereas longer helical peptide undergoes

considerable structural changes upon interaction with CNT.

Thus small globular proteins having smaller helices may be

less affected whereas proteins having longer helices may be

considerably disturbed by the introduction of CNT into the

biological systems. The above-mentioned results are based

on the interaction pattern of PA (homopolymeric helix)

based peptides which forms very stable helix. However, in a

real life scenario, both the sequence and composition of the

helix (heteropolymeric helix) play vital roles in determining

the stability of the helix as shown in our previous study.14

Overall results show that the stability of the helical peptide in

isolated conditions is completely different from that at the

nanomaterial interface. Comparison of results shows

obtained from the MD simulation of CNT-ChainH and

CNT-Supercoil systems reveal that structural perturbations

in the isolated helical fragment are higher than those in

supercoiled helix. It is interesting to note that structure (hel-

icity) of helical chain in supercoiled bundle does not change

appreciably upon interaction with CNT. Both the length of

the helical peptide and the inherent structural stability of the

helical unit in the supercoiled helix influence the interaction

pattern with the CNT.

The authors thank Dr. C. N. Patra and Dr. S. K. Ghosh, BARC, for

their valuable suggestions and comments. The authors also thank

Dr. T. Ramasami, Secretary, DST, GOI, and Dr. A. B. Mandal, Direc-

tor, CSIR-CLRI for their continued support.

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FIGURE 12 van der Waals interaction between CNT-Peptide system and Electrostatic interaction

within the peptide during the simulation time. (A) CNT-Chain_H and (B) CNT-Supercoil.


Biopolymers

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Reviewing Editor: Eric J. Toone


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Length-dependent stability of α-helical peptide upon adsorption to single-walled carbon nanotube