Biophysical Chemistry 297 (2023) 107011

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Biophysical Chemistry
journal homepage: www.elsevier.com/locate/biophyschem

Exploring the aggregation of amyloid-β 42 through Monte

Carlo simulations
Priya Dey , Parbati Biswas *
Department of Chemistry, University of Delhi, Delhi 110007, India

A R T I C L E I N F O A B S T R A C T

Keywords: Coarse-grained Monte Carlo simulations are performed for a disordered protein, amyloid-β 42 to identify the
Metropolis Monte Carlo simulations interactions and understand the mechanism of its aggregation. A statistical potential is developed from a selected
Coarse grained Cα chain backbone model dataset of intrinsically disordered proteins, which accounts for the respective contributions of the bonded and
Intrinsically disordered proteins
non-bonded potentials. While, the bonded potential comprises the bond, bend, and dihedral constraints, the
Aggregation propensity
Non-local contacts
nonbonded interactions include van der Waals interactions, hydrogen bonds, and the two-body potential. The
PMF profile two-body potential captures the features of both hydrophobic and electrostatic interactions that brings the chains
at a contact distance, while the repulsive van der Waals interactions prevent them from a collapse. Increased two-
body hydrophobic interactions facilitate the formation of amorphous aggregates rather than the fibrillar ones.
The formation of aggregates is validated from the interchain distances, and the total energy of the system. The
aggregate is structurally characterized by the root-mean-square deviation, root-mean-square fluctuation and the
radius of gyration. The aggregates are characterized by a decrease in SASA, an increase in the non-local in­
teractions and a distinct free energy minimum relative to that of the monomeric state of amyloid-β 42. The
hydrophobic residues help in nucleation, while the charged residues help in oligomerization and aggregation.

1. Introduction
Proteins are susceptible to misfolding in a heterogeneous intracel­
lular environment, where they are locally trapped in some of the low-
energy near-native conformations rather than the thermodynamically
stable functional native state, which represents the free energy mini­
mum in the folding energy landscape [1,2]. These misfolded proteins
tend to associate to form dimers and oligomers, which subsequently self-
assemble as fibrillar aggregates with characteristic cross beta-sheet
structures known as amyloids [3]. The formation of these fibrils in
vitro are a generic attribute of many proteins, especially intrinsically
disordered proteins, under specified experimental conditions. Intrinsi­
cally disordered proteins do not fold to a unique native structure but
rather exist as a dynamic ensemble of interconvertible conformations
[4]. Such proteins are mostly amyloidogenic and readily form amyloids
[5]. Amyloids are highly toxic and disrupt the normal physiological
functioning of the cell [6]. Protein aggregation is often implicated in a
broad spectrum of debilitating human disorders, that comprise more
than 50 identified neurodegenerative diseases like Alzheimer's, Parkin­
son's, Huntington's diseases, type 2 diabetes and some forms of cancer.
However, functional amyloids also exist in other forms of life like bac­
teria and fungi [7]. Specifically, Alzheimer's disease is caused by the
aggregation of the intrinsically disordered protein amyloid-β, which is
derived from the amyloid precursor protein.
Amyloid-β (Aβ) is a 40 or 42 residue protein that causes Alzheimer's
disease via the formation of soluble oligomers, which is reported to be
the principal cytotoxic species as compared to the mature fibrils [8].
However, in-vitro studies have demonstrated a significantly higher rate
of fibril formation in Aβ − 42 as compared to that of Aβ − 40 [9–11].
Oligomers may be either structured or unstructured. Since oligomers are
difficult to characterize experimentally, computer simulations and ki­
netic models are employed to provide significant insights regarding the
structure, stability and the potential mechanism of Aβ − 42 aggregation
[12].
Protein aggregation involves a multitude of both length and time
scales that may be interpreted via a hierarchy of models ranging from
simple coarse-grained models to the precise atomistic ones. [13]. Ag­
gregation of protein monomers and oligomers were extensively studied
using all-atom molecular dynamics simulations [14,15]. Such calcula­
tions are however limited due to the high computational cost imposed

* Corresponding author.
E-mail address: pbiswas@chemistry.du.ac.in (P. Biswas).

https://doi.org/10.1016/j.bpc.2023.107011
Received 3 February 2023; Received in revised form 25 March 2023; Accepted 26 March 2023
Available online 5 April 2023
0301-4622/© 2023 Elsevier B.V. All rights reserved.
P. Dey and P. Biswas Biophysical Chemistry 297 (2023) 107011

by the size of the system and sampling of the protein conformational

space. Therefore, coarse-grained models of proteins at varying levels of
details constitute an essential component for exploring various generic
features of protein aggregation [16]. Such studies primarily investigated
the factors leading to fibril nucleation and formation. The precise
mechanism of aggregation is protein specific and varies from one protein
to the other. Atomistic simulations both with and without solvent are
used to probe the early events of the aggregation process for small
proteins [17,18]. Several simulation studies have been done on mono­
mers [19–21], formation of dimers [22] and oligomers [23,24], amyloid
fibril elongation [25,26] and amyloid fibril stability [27–29]. Recent
molecular dynamics (MD) simulation studies of Aβ − 42 and Aβ frag­
ments have shown that a β-hairpin structure promotes the formation of
intermolecular β-sheet structures [30,31]. A lattice model was devel­
oped to study protein aggregation in three-dimensional cubic lattices
using MC simulations [32] to investigate an interplay between amor­
phous aggregation and fibril formation. The oligomerization of Aβ
(16–22) peptides was explored using Metropolis MC simulations, which
demonstrated the spontaneous formation of low energy aggregates like
small oligomers and fibril-like structures [33]. Some simulation studies
have also confirmed that oligomers are more neurotoxic than amyloid
fibrils [34–36].
In this work, aggregation of the intrinsically disordered protein,
amyloid-β 42 is investigated via Metropolis [37] Monte Carlo simulation
algorithm based on a coarse-grained Cα chain backbone model [38]. A
coarse-grained statistical potential is developed that captures the salient
features of aggregation through hydrophobic effect, hydrogen bonding,
electrostatic and nonbonded interactions. The formation of protein ag­
gregates is analyzed by evaluating various structural properties like the
root-mean-square deviation (RMSD), root-mean-square fluctuation
(RMSF) and the radius of gyration (Rg), while the role of the non-bonded
interactions are quantified in terms of the intrachain and interchain
residue contacts. The structural transition from an extended monomeric
chain to a compact aggregate is reflected in the variation of the
conformational properties. The specific roles of the local and nonlocal
interactions in protein aggregation are investigated while the free en­
ergy profile is calculated from the potential of mean force. Fig. 1. Protein chain systems contained in the box with various size to keep the
system concentrations constant.
2. Methodology
DISPROT database is used to design a statistical potential that comprises
A coarse-grained Cα chain backbone model of the amyloid-β 42 both bonded and non-bonded contributions due to both interchain and
protein is considered where a residue is represented by a single Cα atom intrachain residue interactions. [41]. The bonded interactions include
while the side-chain conformations are neglected. The initial structure the energy function that accounts for the bond stretches, bond angles
of monomeric amyloid-β 42 (Aβ-42) protein is selected from the and dihedrals. These interactions are modeled as suitable constraints
Research Collaboratory for Structural Bioinformatics (RCSB) PDB with [42]. A data-set of 1135 intrinsically disordered proteins [43] is
the PDB ID:1Z0Q. Aβ-42 is derived by successive endoproteolytic pro­ compiled from the RCSB PDB and the distribution of bond lengths, Cα(i) -
cessing of the transmembrane amyloid precursor protein (APP) by β- and Cα(i + 1), bond angles Cα(i) - Cα(i + 1) - Cα(i + 2) and the dihedral angles,
γ-secretases [39]. The sequence of the amyloid-β 42 monomer is Cα(i) - Cα(i + 1) - Cα(i + 2) - Cα(i + 3) between all constituent residues are
‘DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA'. Since calculated.
simulations of a single monomeric chain does not capture the interchain The range of the pseudo bond lengths and pseudo bend angles be­
interactions that lie at the core of the aggregation process, multi-chain tween the neighboring Cα backbone atoms is calculated from Fig. S1 and
systems are prepared using Packmol software [40]. The number den­ Fig. S2 of the Supplementary Material as 3.65–4.10 Å and 75◦ –160◦ ,
sity of the monomeric chains in the simulation box is kept constant, respectively. To restrict the dihedral angle, three most populated regions
which fixes the concentration of the system as shown in Fig. 1. The 10◦ –70◦ , 160◦ –180◦ and (− 180◦ ) – (− 100◦ ) are accessed and sampled
relevant information about the dimension of the boxes and the number from the distribution plots (refer to Fig. S3 of the Supplementary Ma­
density is given in Table S1 of the Supplementary Material. Systems with terial). The non-bonded interactions include van der Waals interactions,
two to eight chains are simulated and examined, while the findings for hydrogen bonding [44,45], and the distance dependent pairwise in­
the dimer, trimer and tetramer are analyzed and discussed. teractions between the non-bonded residues [46].

2.1. Potential 2.2. van der Waals interactions

The development of an appropriate force field is a key step in protein
aggregation. Since most force fields were developed for the globular
proteins rather than the intrinsically disordered proteins (IDPs), sec­
ondary structures in the unfolded or misfolded states of IDPs is exces­
sively stabilized. Therefore, a selected data set of IDPs compiled from the
A 6–12 Lennard-Jones potential [47,48] is used to model the van der
Waals interactions between the intrachain and interchain residues,
which may be expressed as

2
P. Dey and P. Biswas
[( ) ( )6 ]
12
rmin rmin
EVDW =ε − 2
rij rij
where EVDW denotes the van der Waals interaction potential between the
i-th and j-th residues separated by a spatial distance of rij and ε is the
depth of the energy well, which is assumed to be 1 for simplicity. The
distance between two particles at which the potential is minimum is
given by rmin.
2.3. Hydrogen bonding
A 10–12 Lennard-Jones potential is employed for modeling the
hydrogen bond potential as proposed by Scheraga and co-workers,
which may be given by [44].
[ ( )12 ( )10 ]
Rmin Rmin
EHB = ε 5 − 6 (2)
rij rij
where Rmin is the spatial distance between the residues for which the
hydrogen bond potential is minimum and ε is the depth of the potential
well, which is assumed to be unity. This coarse-grained model accounts
only for the Cα backbone-backbone hydrogen bond where the explicit
nature of the side chains is neglected. The formation of a hydrogen bond
between a pair of residues must satisfy a bond length and a bond angle
constraint. The distance between the backbone N atom of a residue and
the backbone O atom of another residue should be ≤3.5 Å and the CON
angle should be >90◦ . The value of Rmin is obtained by evaluating the Cα
− Cα backbone distances between the residues that form the hydrogen
bond, obtained from the selected data-set of 1135 intrinsically disor­
dered proteins. The minimum distance, Rmin, is defined to be the value
that corresponds to the peak at 5.25 Å in the plot of the distribution of
residue-residue distances forming the hydrogen bond (refer to Fig. S4 of
Supplementary Material). Thus, hydrogen bond is formed between two
residues if the two interacting resides are at a distance of 5.0–7.0 Å in the
Cα chain backbone model.
2.4. Two-body potential
Two-body interaction potential determines the non-bonded in­
teractions between any two residues along the sequence of the protein.
The effective two-body potentials between residues are obtained from a
distribution of the pairwise distances between them using the data set of
1135 intrinsically disordered proteins [43].
Two-body interaction potential for the Cα chain backbone model is
derived from the selected dataset of proteins, where the Cα atom is
residue-specific indicating the Cα of one residue is different from that of
the other. Hence, there are 20 different atom types forming 210 distinct
atom pairs for the two-body potential calculations. The separation be­
tween a residue pair is calculated using distance shells which starts at
1.5 Å from any residue in the pair, with each shell at a radial distance of
1 Å in width as shown in Fig. 2. For instance, the third distance shell
covers the distance from 3.5 to 4.5 Å, while the thirtieth distance shell
maps the distance from 30.5 Å to infinity. This two-body potential in­
corporates both electrostatic and hydrophobic interactions. The poten­
tial for any residue pair, i and j, within a distance shell d, is defined using
Boltzmann inversion method [49] as
[ ]
N(i, j, d)obs
E2B (i, j, d) = − ln
N(i, j, d)exp
where N(i, j, d)obs and N(i, j, d)exp are the number of interacting pairs of
residues observed and the maximum number of such interacting residue
pairs expected in the distance shell d, respectively. N(i, j, d)obs is evalu­
ated by computing the number of residue pairs i and j in a particular
distance shell d, while N(i, j, d)exp is calculated from
Biophysical Chemistry 297 (2023) 107011
(1)
Fig. 2. Schematic representation of two-body intrachain and inter­
chain potential.
N(i, j, d)exp = N(d)χ i χ j (4)
where N(d) is the total number of interacting residue pairs and χ k is the
mole fraction of k-th type of residue derived from the total mole frac­
tions of the distinct residue types in the overall data-set. Two-body po­
tential is estimated for all residue pairs using the selected data-set of
1135 IDPs as shown in Fig. 3. Most of the residue pairs have a lower
probability of non-bonded contact in the first and second distant shells
resulting in lower potential values. However, two-body contact in­
teractions between any two residues commence at larger distance shells
4, 5, and 6. For larger distance shells, there is a higher probability of
contact between the residue pairs and most residue pairs exhibit an
attractive interaction. The hydrophobic residue pairs in contact pri­
marily experience attractive interactions, whereas the hydrophilic con­
tact residue pairs exhibit repulsive interactions. The characteristics of
the two-body potential are presented in Figs. 4 and 5 for different pairs
of residues. Fig. 4 illustrates the striking contrast of the two-body po­
tential between the pairs of Leu-Ile and Leu-Asp residue pairs. A distinct
potential well is observed for the pair Leu-Ile, which indicates the
attractive interaction present in the hydrophobic residue pair revealing
its hydrophobic characteristics, however no such pattern is observed for
the Leu-Asp residue pair.
The two-body potential of the charged residues is also plotted versus
the number of distance shells in Fig. 5. The attractive interactions be­
tween the oppositely charged residue pair Asp-Lys may be observed,
while a repulsive interaction between the similarly charged residue pairs
Asp-Asp and Lys-Lys is noted, which highlights the role of electrostatic
interactions.
Thus, the total energy of the system is given by
E = EVDW + EHB + E2B (5)
(3)
The Cα chain backbone model of the dimer, trimer and tetramer of
amyloid-β is selected and the chains are positioned randomly at a dis­
tance of 35 Å. The initial energy is calculated using Eq. (5). At each MC
step, a random residue is selected and moved to a new position. The
energy of this newly generated conformation is calculated after applying
appropriate restrictions in the bond length, bend angle and dihedral
angle to obtain real protein conformations. The concentration is
3
P. Dey and P. Biswas
Fig. 3. The representation of residue-based pairwise two-body potential for the distance shells 1, 2, 3, 4, 5, 6, 8, 10, 15 and 30.
Fig. 4. The two-body interaction potentials between hydrophobic residue pair
Leu-Ile and between hydrophobic and hydrophilic residue pair Leu-Asp.
Fig. 5. The two-body interaction potentials between oppositely charged res­
idue pair Asp-Lys and between similarly charged residues pairs Lys-Lys and
Asp-Asp. Each distance shell is 1 Å wide.
4
Biophysical Chemistry 297 (2023) 107011
maintained using a PBC (periodic boundary condition) [50]. The newly
generated conformation is selected according to the Metropolis criterion
[51]. Any residue is moved using the Boltzmann probability, PT = exp
(-Eij/kBT), where Eij = Ej − Ei is the difference in energy between its new
(Ej) and old (Ei) conformations, T is the absolute temperature and kB is
Boltzmann constant. The Monte Carlo move is accepted if the initial
energy is more than that of the newly generated conformation, other­
wise the move is accepted conditionally. Then, a random number
generator subroutine ran1(idum) [52] is employed to produce a pseudo
random number which is compared with the the transition probability,
PT. The Monte Carlo move is accepted for PT > pseudo-random number,
otherwise the move is rejected. A unit Monte Carlo (MC) step is an
attempt to move a residue once.
3. Results and discussion
The total energy of the dimer, trimer and tetramer is calculated from
Eq. (5) and plotted as a function of the number of MC steps as shown in
Fig. S6 of the Supplementary Material. The energy of the dimer, trimer
and tetramer decreases with an increase in the number of MC moves and
attains equilibrium due to the formation of a stable aggregate. The
components of the total energy is calculated using Eqs. (1), (2) and (3)
and are presented in Figs. 6 (a), Figs. 6 (b) and Figs. 6 (c) for Lennard-
Jones potential, Two-body potential and Hydrogen bond potential of
the dimer, trimer and tetramer of amyloid-β, respectively.
The two-body distance-dependent interaction potential captures the
features of both hydrophobic and electrostatic interactions. A higher
value of the two-body potential leads to increased hydrophobic in­
teractions due to the presence of more than 45% hydrophobic residues
in amyloid-β. The strength of hydrophobic interactions dominates that
of the hydrogen bond potential, which results in the formation of
amorphous rather than fibrillar aggregates as observed in earlier studies
[14,53] since hydrophobic interactions lead to the formation of amor­
phous aggregates [54]. The generation of fibrils involves the trans­
formation of small amorphous aggregates →β-sheets → ordered-nucleus
which leads to a formation of a stable fibril nucleus [14]. Consequently,
the two-body potential is initially attractive for the inter and intrachain
interactions which helps in bringing the chains to a contact distance,
P. Dey and P. Biswas Biophysical Chemistry 297 (2023) 107011

Fig. 6. Variation of different components of total energy, i.e. Lennard-Jones potential, Two-body potential and Hydrogen bond potential for dimer, trimer and
tetramer of amyloid-β with MC moves.

Fig. 7. The intrachain and interchain contacts in the dimer, trimer and tetramer of amyloid-β 42.

5
P. Dey and P. Biswas
while the repulsive van der Waals interaction prevents the chains from
collapsing.
The intrachain and interchain contact map provides a statistical
description of the three-dimensional organization of dimer, trimer and
tetramer structures. Two residues are considered to be in contact when
the spatial distance of separation between them is ≤7.5 Å [55]. In Fig. S7
of the Supplementary Material, the probability contact map for the
trimer is shown. The intrachain contacts are observed in the initial
conformations of the protein due to the contacts between the neigh­
boring residues, however both the intrachain and the interchain contacts
are found in the later conformations as a function of MC steps (for the ith
residue, (i + 1)th and (i − 1)th residue are the neighboring residues). The
three different chains of the trimer are represented as ‘chain A', ‘chain B'
and ‘chain C'. It is observed that interchain contacts (i.e. between chain
A and chain B or chain B and chain C) are also formed along with the
intrachain contacts. However, the interchain interactions lead to the
aggregate formation.
Fig. 7 reflects a marked increase in the number of numerous inter­
molecular hydrophobic contacts and intramolecular contacts for some
residues as a function of the MC steps. The formation of the aggregates as
dimer, trimer or tetramer of amyloid-β is primarily driven by the energy
gain associated with an increase in the number of intermolecular hy­
drophobic contacts. This is in agreement with a previous simulation
study [56].
The change in the structure of a protein during simulations can be
quantified through the radius of gyration, Rg, which is defined as:
√̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅
√ N
√∑ (r(i) − rc )2
Rg = √ (6)
N phobic residues in the dimer, trimer and tetramer of the amyloid-β
n=1
where N is the number of protein atoms and r(i) and rc are the co­
ordinates of an ith residue and the center of mass, respectively. The
variation of the radius of gyration with simulation steps is shown in
Fig. S8 of the Supplementary Material. The sharp decrease in Rg due to
the formation of aggregates of protein chains provides an evidence that
the extended structure gradually collapsed.
The root-mean-square deviation (RMSD) for the dimer, trimer and
the tetramer of amyloid-β is monitored to measure of convergence of the
MC simulation runs. RMSD is defined as:
√̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅
∑N
i=1 (ri (t) − ri (0) )
RMSD(t) = (7)
N
where N is the number of protein atoms and ri(t) and ri(0) denote the
position coordinates of the ith atom of the initial structure and the
structure after the tth MC step respectively.
The evolution of RMSDs with the Monte Carlo moves of the dimer,
trimer and tetramer of amyloid-β is shown in Fig. S8 of the Supple­
mentary Material. The RMSD become stable after 5 × 107 MC steps for
the dimer, trimer and tetramer of amyloid-β indicating that the dimer or
oligomers formed are stabilized. The RMSD values for the dimer of
Fig. 8. Variation in the distance between the chains of dimer, trimer and tetramer with MC moves.
6
Biophysical Chemistry 297 (2023) 107011
amyloid-β reproduce the data reported earlier [57].
The interchain distances in terms of the centre of mass distance, are
calculated. Fig. 8 shows a decrease in the distance between the two
chains with an increase in the MC simulation steps which indicates
increasing interchain interactions with the subsequent formation of the
aggregate.
The root mean-square fluctuation (RMSF) of the Cα atoms is
computed in order to quantify the magnitude of deviation from their
respective average positions for the specific sites along the backbone of
the dimer, trimer, and tetramer of amyloid-β.
It is defined as
√̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅̅
( )2̅
√
√1 ∑ N
1 ∑ N
RMSF = √ rj,i − rk,i (8)
N j=1 N k=1
Larger RMSF value indicates increased flexibility, whereas low RMSF
values show restricted movements during simulation about its average
position.
In the dimer, trimer and tetramer, individual residues of various
chains fluctuate in distinct ways. This finding demonstrates substantial
fluctuations of the N- or C-terminal residues that indicate local unfold­
ing. Analysis of the flexibility shows that the residue fluctuations in­
crease with an increase in the number of chains as shown in Fig. 9. The
RMSF is also plotted based on the amino acid type present in the dimer,
trimer and tetramer as shown in Fig. S9 of the Supplementary Material.
It is observed that the charged residues fluctuate more than the hydro­
phobic residues in the dimer and the cumulative effect of the negatively
and positively charged residues are more pronounced than the hydro­
protein. This shows that the charged residues play a significant role in
the formation of aggregates as shown in Fig. 10. This is in agreement
with an earlier work [58] suggesting that the behaviour of positively and
negatively charged residues has a substantial impact on the hydropho­
bicity of the protein that determines its aggregation propensity [59].
In Fig. 11, the local and nonlocal contacts are calculated for the
dimer, trimer and tetramer for the Cα chain backbone coarse grained
model of amyloid-β. Local contact measures the contact between the
nonbonded residues up to the (i + 4)th position along the sequence. The
number of contacts between non-bonded residues within a threshold
distance of 7.5 Å separated by more than (i + 4) residues in the sequence
represents nonlocal contact [38]. It is observed that the aggregation of
the dimer, trimer, and tetramer of amyloid-β is initially regulated by the
local contacts. However, With the progress of simulation, the nonlocal
interactions play a more significant role resulting in increasing contacts
between the residues of the dimer, trimer and tetramer of the amyloid-β.
It may be due to this reason that the aggregation takes place when some
of the most strongly interacting amino acids form local contacts which
lead to the formation of a specific subset of the native structure [60].
These structures provide a seed for the aggregation process and may be
considered as partially folded intermediates that are involved in the
aggregation of a number of proteins [61,62]. Thus, formation of
P. Dey and P. Biswas Biophysical Chemistry 297 (2023) 107011

Fig. 9. Root-mean square fluctuation, RMSF of the dimer, trimer and tetramer of amyloid-β as a function of MC moves at different time scales.

Fig. 10. Normalised Root-mean square fluctuation, RMSF, for the hydrophobic and charged residues present in the dimer, trimer and tetramer of amyloid-β.

aggregates primarily occur due to the nonlocal interactions.
The solvent-accessible surface area (SASA) is calculated using the
PCASA software [63] which is a rapid SASA estimator for coarse-grained
models and is shown in Fig. S10 of the Supplementary Material for the
trimer of amyloid-β. A higher value of the SASA is correlated with the
extended chains in the trimer of amyloid-β. A decrese in the SASA is
observed for the aggregates relative to that of the monomeric form
which may be due to the formation of a compact structure of the trimer
of amyloid-β.
The free energy profile was calculated from the potential of mean
force. The potential of mean force (PMF) at any coordinate can be
calculated by averaging over the forces for specific position coordinates
(such as center to center interchain distances) for the dimer, trimer and
tetramer of amyloid-β. The potential of mean force may be expressed as
[64,65]:
U(r) = − kB Tln(g(r) ) (9)
where g(r) denotes the radial distribution function from the centre of
mass of one chain to that of the other for the dimer, trimer and tetramer
of amyloid-β. A dimer or oligomer of amyloid-beta is formed when the

7
P. Dey and P. Biswas Biophysical Chemistry 297 (2023) 107011

Fig. 11. Variation in local and nonlocal contacts of the (a)dimer, (b) trimer and (c) tetramer with the MC moves.

Fig. 12. The plot of the potential of mean force for the dimer, trimer and tetramer of amyloid-β.

CoM of the chains are separated by a distance of 4.5–5.5 Å as shown in 4. Conclusions

Fig. 12. The aggregate of amyloid-β appears as a narrow well located on
the the left-hand side of the PMF profile. The energy landscape is typi­
cally rugged, which represents an ensemble of closely spaced confor­
mations that may belong to the misfolded states [66,67]. These
misfolded proteins through intermolecular interactions form amorphous
aggregates, which are defined as a supramolecular assembly of poly­
peptide chains without a defined shape [54,68]. Thus, the PMF profile
exhibits a narrow basin corresponding to the formation of stable ag­
gregates. The plots of the energy, Rg, RMSD, RMSF and the free energy
profiles are shown for the pentamer, hexamer, heptamer and octamer of
amyloid-β respectively in Figs. S11 - S15 of the Supplementary Material.
A coarse-grained Monte Carlo approach is used to investigate the
mechanism which leads to the protein aggregation. The development of
an accurate force field is one of the most important steps in under­
standing protein aggregation. This potential is modeled in terms of the
bonded and non-bonded interactions using a selected data-set of
intrinsically disordered proteins, since protein force fields developed for
folded proteins produce highly compact structures for IDPs. The bonded
potential is modeled in terms of the bond, bend and dihedral restrictions,
while the non-bonded interactions is comprise the van der Waals,
hydrogen bond and two-body potential. The two-body potential be­
tween the atoms of the hydrophobic residues, Leu and Ile indicates
attractive interactions between them and like-charged hydrophilic

8
P. Dey and P. Biswas
residues show a repulsive two body interaction, while oppositely
charged hydrophilic residues show an attractive two body interaction.
The two-body potential comprises an attractive interchain and intra­
chain interaction and helps to bring the chains at the contact distance,
while the repulsive van der Waals interaction keeps the chains from
collapsing. The total energy of the dimer, trimer and tetramer of amy­
loid-β decreases with an increase in the Monte Carlo moves confirming
the formation of the amorphous oligomer. The structural properties of
the aggregate are characterized through the root-mean-square deviation
(RMSD), root-mean-square fluctuation (RMSF), the radius of gyration
(Rg) and the PMF profile, while the role of interactions may be eluci­
dated by calculating the contacts formed by intra- and interchain resi­
dues respectively. The hydrophobic residues help in nucleation, while
the charged residues promote oligomerization and aggregation. The
transition from an extended structure to a compact form is exhibited by a
decrease in the solvent-accessible surface area and the PMF profile ex­
hibits a narrow basin corresponding to the formation of stable aggre­
gates. This method may be modified to enhance our understanding
regarding the secondary structural changes that occurs during the ag­
gregation of intrinsically disordered proteins.
CRediT authorship contribution statement
Priya Dey: Data curation, Formal analysis, Validation, Writing -
original draft. Parbati Biswas: Conceptualization, Methodology, Su­
pervision, Validation, Writing - original draft, Writing - review &
editing.
Declaration of Competing Interest
The authors declare no competiting financial interest.
Acknowledgments
The authors gratefully acknowledge DST-SERB, India (project no.
CRG/2022/000889) and the FRP Grant-IoE (Ref. No. IoE/2021/12/
FRP) for financial support. Priya Dey acknowledges CSIR, India, for
providing financial support in the form of a Senior Research Fellowship
(09/045(1536)/2017-EMR-I).
Appendix A. Supplementary data
Supplementary data to this article can be found online at https://doi.
org/10.1016/j.bpc.2023.107011.
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