The metastable states of proteins

DK Ghosh, A Ranjan - Protein Science, 2020 - Wiley Online Library
The intriguing process of protein folding comprises discrete steps that stabilize the protein
molecules in different conformations. The metastable state of protein is represented by …

Differential Effects of Sequence-Local versus Nonlocal Charge Patterns on Phase Separation and Conformational Dimensions of Polyampholytes as Model …

T Pal, J Wessén, S Das, HS Chan - The Journal of Physical …, 2024 - ACS Publications
Conformational properties of intrinsically disordered proteins (IDPs) are governed by a
sequence-ensemble relationship. To differentiate the impact of sequence-local versus …

Dilute semiflexible polymers with attraction: Collapse, folding and aggregation

J Zierenberg, M Marenz, W Janke - Polymers, 2016 - mdpi.com
We review the current state on the thermodynamic behavior and structural phases of self-
and mutually-attractive dilute semiflexible polymers that undergo temperature-driven …

Multistep molecular mechanisms of Aβ16-22 fibril formation revealed by lattice Monte Carlo simulations

PH Nguyen, P Derreumaux - The Journal of Chemical Physics, 2023 - pubs.aip.org
As a model of self-assembly from disordered monomers to fibrils, the amyloid-β fragment
Aβ16-22 was subject to past numerous experimental and computational studies. Because …

Metastable alpha‐rich and beta‐rich conformations of small Aβ42 peptide oligomers

PH Nguyen, F Sterpone… - … : Structure, Function, and …, 2023 - Wiley Online Library
Probing the structures of amyloid‐β (Aβ) peptides in the early steps of aggregation is
extremely difficult experimentally and computationally. Yet, this knowledge is extremely …

Shape-free theory for the self-assembly kinetics in macromolecular systems

LF Trugilho, LG Rizzi - Europhysics Letters, 2022 - iopscience.iop.org
Although temperature-dependent self-assembly kinetics is usually described by approaches
which assume that the macromolecular aggregates have a definite shape, sometimes that …

Amyloid fibril solubility

LG Rizzi, S Auer - The Journal of Physical Chemistry B, 2015 - ACS Publications
It is well established that amyloid fibril solubility is protein specific, but how solubility
depends on the interactions between the fibril building blocks is not clear. Here we use a …

[PDF][PDF] The interplay of intrinsic disorder and macromolecular crowding on α-synuclein fibril formation

NC Shirai, M Kikuchi - Biophysical Journal, 2016 - cell.com
We focused on the relation between the intrinsic disorder of α-syn and macromolecular
crowding, and constructed a lattice gas model of α-syn including crowding agents based on …

Microcanonical thermostatistics of aggregation transition in a system with anisotropically interacting molecules

LF Trugilho, LG Rizzi - Journal of Physics: Conference Series, 2020 - iopscience.iop.org
Microcanonical thermostatistics analysis has been introduced as an important method in the
study of phase transitions observed in intrinsically small systems, such as folding transitions …

From particle condensation to polymer aggregation

W Janke, J Zierenberg - Journal of Physics: Conference Series, 2018 - iopscience.iop.org
We draw an analogy between droplet formation in dilute particle and polymer systems. Our
arguments are based on finite-size scaling results from studies of a two-dimensional lattice …