A new theoretical approach to biological self-assembly
M Kinoshita - Biophysical reviews, 2013 - Springer
Upon biological self-assembly, the number of accessible translational configurations of
water in the system increases considerably, leading to a large gain in water entropy. It is …
water in the system increases considerably, leading to a large gain in water entropy. It is …
Energetics of oligomeric protein folding and association
CM Doyle, JA Rumfeldt, HR Broom, A Broom… - Archives of biochemistry …, 2013 - Elsevier
In nature, proteins most often exist as complexes, with many of these consisting of identical
subunits. Understanding of the energetics governing the folding and misfolding of such …
subunits. Understanding of the energetics governing the folding and misfolding of such …
Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition
It is a central issue to elucidate the new type of molecular recognition accompanied by a
global structural change of a molecule upon binding to its targets. Here we investigate the …
global structural change of a molecule upon binding to its targets. Here we investigate the …
Anomalously rapid hydration water diffusion dynamics near DNA surfaces
The emerging Overhauser effect dynamic nuclear polarization (ODNP) technique measures
the translational mobility of water within the vicinity (5–15 Å) of preselected sites. The work …
the translational mobility of water within the vicinity (5–15 Å) of preselected sites. The work …
A machine learning approach for hot-spot detection at protein-protein interfaces
Understanding protein-protein interactions is a key challenge in biochemistry. In this work,
we describe a more accurate methodology to predict Hot-Spots (HS) in protein-protein …
we describe a more accurate methodology to predict Hot-Spots (HS) in protein-protein …
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins
Motivation: To assess whether two proteins will interact under physiological conditions,
information on the interaction free energy is needed. Statistical learning techniques and …
information on the interaction free energy is needed. Statistical learning techniques and …
Structure of the ultra-high-affinity colicin E2 DNase–Im2 complex
How proteins achieve high-affinity binding to a specific protein partner while simultaneously
excluding all others is a major biological problem that has important implications for protein …
excluding all others is a major biological problem that has important implications for protein …
Valid entropy–enthalpy compensation: Fine mechanisms at microscopic level
EB Starikov - Chemical Physics Letters, 2013 - Elsevier
If the physically–chemically valid entropy–enthalpy compensation (EEC) could be revealed
in experiments, what are then its actual mechanisms at the atomic/molecular level? This …
in experiments, what are then its actual mechanisms at the atomic/molecular level? This …
Using machine‐learning‐driven approaches to boost hot‐spot's knowledge
Understanding protein–protein interactions (PPIs) is fundamental to describe and to
characterize the formation of biomolecular assemblies, and to establish the energetic …
characterize the formation of biomolecular assemblies, and to establish the energetic …
Structural stability of proteins in aqueous and nonpolar environments
S Yasuda, H Oshima, M Kinoshita - The Journal of chemical physics, 2012 - pubs.aip.org
A protein folds into its native structure with the α-helix and/or β-sheet in aqueous solution
under the physiological condition. The relative content of these secondary structures largely …
under the physiological condition. The relative content of these secondary structures largely …