Hydrophobic‐hydrophilic forces in protein folding

SR Durell, A Ben‐Naim - Biopolymers, 2017 - Wiley Online Library
The process of protein folding is obviously driven by forces exerted on the atoms of the
amino‐acid chain. These forces arise from interactions with other parts of the protein itself …

Computational insights into the role of α-strand/sheet in aggregation of α-synuclein

A Balupuri, KE Choi, NS Kang - Scientific Reports, 2019 - nature.com
The α-synuclein is a major component of amyloid fibrils found in Lewy bodies, the
characteristic intracellular proteinaceous deposits which are pathological hallmarks of …

Temperature dependence of hydrophobic and hydrophilic forces and interactions

SR Durell, A Ben-Naim - The Journal of Physical Chemistry B, 2021 - ACS Publications
Molecular dynamics simulations are used to compare the forces and Gibbs free energies
associated with bringing small hydrophobic and hydrophilic solutes together in an aqueous …

Properties of spanning water networks at protein surfaces

N Smolin, A Oleinikova, I Brovchenko… - The Journal of …, 2005 - ACS Publications
The formation of a spanning two-dimensional hydrogen-bonded water network at the
surface of proteins via a percolation transition enables their biological function. We show in …

Kinetics and thermodynamics of type VIII β-turn formation: a CD, NMR, and microsecond explicit molecular dynamics study of the GDNP tetrapeptide

PFJ Fuchs, AMJJ Bonvin, B Bochicchio, A Pepe… - Biophysical journal, 2006 - cell.com
We report an experimental and theoretical study on type VIII β-turn using a designed peptide
of sequence GDNP. CD and NMR studies reveal that this peptide exists in equilibrium …

A novel main chain motif in proteins bridged by cationic groups: the niche

GM Torrance, DP Leader, DR Gilbert… - Journal of Molecular …, 2009 - Elsevier
We have surveyed the bridging of pairs of main chain carbonyl oxygens by cations or by δ+
hydrogens within hydrogen bonding groups. A three to four residue motif, which we call the …

Exploring Conformational Preferences of Leu-enkephalin Using the Conformational Search and Double-Hybrid DFT Energy Calculations

HS Park, BJ Byun, YK Kang - ACS omega, 2022 - ACS Publications
The conformational preferences of Leu-enkephalin (Leu-Enk) were explored by the
conformational search and density functional theory (DFT) calculations. By a combination of …

Simple one-electron invariants of molecular chirality

AV Luzanov, D Nerukh - Journal of mathematical chemistry, 2007 - Springer
Pseudoscalar measures of electronic chirality for molecular systems are derived using the
spectral moment theory applied to the frequency-dependent rotational susceptibility. In this …

Hamiltonian and distance replica exchange method studies of Met-enkephalin

L Su, RI Cukier - The Journal of Physical Chemistry B, 2007 - ACS Publications
The conformational states of the zwitterionic form of the pentapeptide Met-enkephalin were
explored with the use of explicit solvent molecular dynamics (MD). The N and C termini are …

Transition paths of met-enkephalin from markov state modeling of a molecular dynamics trajectory

R Banerjee, RI Cukier - The Journal of Physical Chemistry B, 2014 - ACS Publications
Conformational states and their interconversion pathways of the zwitterionic form of the
pentapeptide Met-enkephalin (MetEnk) are identified. An explicit solvent molecular …