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In the present work we study and compare unfolding of a small protein, chicken villin headpiece (HP-36) in two different aqueous binary mixtures, namely water-ethanol (EtOH) and water-dimethyl sulphoxide (DMSO). In both the binary mixtures,…
Nanoconfinement effects on water dissociation and reactivity remain controversial, despite their importance to understand the aqueous chemistry at interfaces, pores, or aerosols. The pKw in confined environments has been assessed from…
We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…
Two novel reduced dimensionality (RD) experiments -(4,3)D-hNCOcaNH and (4,3)D-hNcoCANH- have been presented here to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. The experiments basically…
[ This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in The Journal of Chemical Physics, 157, 024504 (2022) and may be found at:…
Characterization of phases of soft matter systems is a challenge faced in many physicochemical problems. For polymorphic fluids it is an even greater challenge. Specifically, glass forming fluids, as water, can have, besides solid…
1H spin-lattice relaxation experiments have been performed for water - Bovine Serum Al-bumin (BSA) mixtures including 20% wt and 40% wt of BSA. The experiments have been carried out in a frequency range encompassing three orders of…
Deep Inelastic Neutron Scattering provides a means of directly and accurately measuring the momentum distribution of protons in water, which is determined primarily by the protons ground state wavefunction. We find that in water confined on…
Aqueous proton transport at interfaces is ubiquitous and crucial for a number of fields, ranging from cellular transport and signaling, to catalysis and membrane science. However, due to their light mass, small size and high chemical…
Proteins are arguably the most important class of biomarkers for health diagnostic purposes. Label-free solid-state nanopore sensing is a versatile technique for sensing and analysing biomolecules such as proteins at single-molecule level.…
In recent decades, computer simulations have found increasingly widespread use as powerful tools of studying phase transitions in wide variety of systems. In the particular and very important case of aqueous systems, the commonly used…
A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the…
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…
The aqueous solvent profoundly influences protein folding, yet its effects are relatively poorly understood. In this study, we investigate the impact of solvation on the folding of lattice proteins by using Monte Carlo simulations. The…
De novo protein structure prediction from amino acid sequence is one of the most challenging problems in computational biology. As one of the extensively explored mathematical models for protein folding, Hydrophobic-Polar (HP) model enables…
Amorphous solid water (ASW) is one of the most widely studied solid phase systems. A better understanding of the nature of inter- and intramolecular forces in ASW is, however, still required to correctly interpret the catalytic role of ASW…
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…
One of the challenges of the proteomic analysis by 2D-gel is to visualize the low abundance proteins, particularly those localized in organelles. An additional problem with nuclear proteins lies in their strong interaction with nuclear…
Confinement can significantly alter fluid properties, offering potential for specific technological applications. However, achieving precise control over the structural complexity of confined fluids and soft matter remains challenging, as…