Related papers: Insights into Protein Unfolding under pH, Temperat…
We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered…
The proteasome is a large biomolecular complex responsible for protein degradation. It is under intense research due to its fundamental role in cellular homeostasis, and tremendous potential for medicinal applications. Recent data from…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
Activated processes such as protein unfolding are highly sensitive to heterogeneity in the environment. We study a highly simplified model of a protein in a random heterogeneous environment, a model of the in vivo environment. It is found…
What can cells gain by using disordered, rather than folded, proteins in the architecture of their skeleton? Disordered proteins take multiple co-existing conformations, and often contain segments which act as random-walk-shaped polymers.…
Using coarse-grained molecular dynamics simulations, we analyze mechanically induced dissociation and unfolding of the protein complex CD48-2B4. This heterodimer is an indispensable component of the immunological system: 2B4 is a receptor…
We perform molecular dynamics simulations under uniaxial tension to investigate the micromechanisms underlying strain hardening in glassy polymers. By decomposing the stress into virial components associated with pair, bond, and angle…
We employ molecular dynamics simulation to study the phase separation and rheological properties of a three-dimensional binary liquid mixture with hydrodynamics undergoing simple shear deformation. The impact of shear intensity on domain…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
Large-scale molecular dynamics simulations of shear deformation under constant pressures of amorphous silicon, PT from low-density-amorphous (LDA) to high-density-amorphous (HDA) Si, and formation of shear bands (SBs) are performed using…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Protein misfolding is implicated in many diseases, including the serpinopathies. For the canonical inhibitory serpin {\alpha}1-antitrypsin (A1AT), mutations can result in protein deficiencies leading to lung disease, and misfolded mutants…
Protein phase transitions govern numerous diseases, including neurodegenerative disorders such as Parkinson's and Alzheimer's. In Parkinson's disease, distinct species of the protein alpha-synuclein undergo phase transitions from highly…
With the help of force spectroscopy, several analytical theories aim at estimating the rate coefficient of folding for various proteins. Nevertheless, a chief bottleneck lies in the fact that there is still no perfect consensus on how does…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
The $\beta$-relaxation associated with the sub-glass transition temperature ($T_{\text{g},\beta}$) is attributed to fast, localised molecular motions which can occur below the primary glass transition temperature ($T_{g\alpha}$). Despite…
Unfolded protein aggregation in cellular system is a problem causing various types of diseases depending on which type unfolded proteins aggregate. This phenomenon of aggregation may take place during production, storage, shipment or…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…