Progress in Multiscale Modeling of Silk Materials

HDA Brough, D Cheneler, JG Hardy - Biomacromolecules, 2024 - ACS Publications
As a result of their hierarchical structure and biological processing, silk fibers rank among
nature's most remarkable materials. The biocompatibility of silk-based materials and the …

N-terminal acetylation preserves α-synuclein from oligomerization by blocking intermolecular hydrogen bonds

B Bu, X Tong, D Li, Y Hu, W He, C Zhao… - ACS chemical …, 2017 - ACS Publications
The abnormal aggregation of α-synuclein (α-Syn) is closely associated with Parkinson's
disease. Different post-translational modifications of α-Syn have been identified and …

Effect of electric field on α-synuclein fibrils: Revealed by molecular dynamics simulations

J Razzokov, S Fazliev, M Makhkamov… - International Journal of …, 2023 - mdpi.com
The self-association of amylogenic proteins to the fibril form is considered a pivotal factor in
the pathogenesis of neurodegenerative diseases, including Parkinson's disease (PD). PD …

On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super‐Gaussian Poisson–Boltzmann model

SK Panday, A Chakravorty, S Zhao… - Journal of …, 2025 - Wiley Online Library
The biomolecules interact with their partners in an aqueous media; thus, their solvation
energy is an important thermodynamics quantity. In previous works (J. Chem. Theory …

Fibrous hydrogels for cell encapsulation: a modular and supramolecular approach

MK Włodarczyk-Biegun, K Farbod, MWT Werten… - PLoS …, 2016 - journals.plos.org
Artificial 3-dimensional (3D) cell culture systems, which mimic the extracellular matrix (ECM),
hold great potential as models to study cellular processes under controlled conditions. The …

Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the β-solenoid structure formed by a silk-like …

B Zhao, MA Cohen Stuart, CK Hall - PLoS Computational Biology, 2017 - journals.plos.org
The β roll molecules with sequence (GAGAGAGQ) 10 stack via hydrogen bonding to form
fibrils which have been themselves been used to make viral capsids of DNA strands …

Nanofibrillar hydrogel scaffolds from recombinant protein‐based polymers with integrin‐and proteoglycan‐binding domains

MK Włodarczyk‐Biegun, MWT Werten… - … Research Part A, 2016 - Wiley Online Library
This study describes the design, production, and testing of functionalized variants of a
recombinant protein‐based polymer that forms nanofibrillar hydrogels with self‐healing …

Heparin as a bundler in a self-assembled fibrous network of functionalized protein-based polymers

MK Włodarczyk-Biegun, CJ Slingerland… - …, 2016 - ACS Publications
Nature shows excellent control over the mechanics of fibrous hydrogels by assembling
protein fibers into bundles of well-defined dimensions. Yet, obtaining artificial materials …

Template‐Free Self‐Assembly of Artificial De Novo Viral Coat Proteins into Nanorods: Effects of Sequence, Concentration, and Temperature

EC Vargas, MAC Stuart, R de Vries… - … A European Journal, 2019 - Wiley Online Library
The self‐assembly of protein polymers is a promising route to prepare sophisticated
functional nanostructures. However, the interplay between protein self‐assembly by itself …

Nanoscale insight into silk-like protein self-assembly: effect of design and number of repeat units

J Razzokov, S Naderi, P Van Der Schoot - Physical biology, 2018 - iopscience.iop.org
By means of replica exchange molecular dynamics simulations we investigate how the
length of a silk-like, alternating diblock oligopeptide influences its secondary and quaternary …