A non-equilibrium approach to allosteric communication

G Stock, P Hamm - … Transactions of the Royal Society B …, 2018 - royalsocietypublishing.org
While the theory of protein folding is well developed, including concepts such as rugged
energy landscape, folding funnel, etc., the same degree of understanding has not been …

Equilibrium versus nonequilibrium peptide dynamics: insights into transient 2D IR spectroscopy

DG Hogle, AR Cunningham… - The Journal of Physical …, 2018 - ACS Publications
Over the past two decades, two-dimensional infrared (2D IR) spectroscopy has evolved from
the theoretical underpinnings of nonlinear spectroscopy as a means of investigating detailed …

[HTML][HTML] Folding free energy landscapes of β-sheets with non-polarizable and polarizable CHARMM force fields

AJ Hazel, ET Walters, CN Rowley… - The Journal of chemical …, 2018 - pubs.aip.org
Molecular dynamics (MD) simulations of peptides and proteins offer atomic-level detail into
many biological processes, although the degree of insight depends on the accuracy of the …

SNARE‐mediated membrane fusion is a two‐stage process driven by entropic forces

ZA McDargh, A Polley, B O'Shaughnessy - FEBS letters, 2018 - Wiley Online Library
SNARE proteins constitute the core of the exocytotic membrane fusion machinery. Fusion
occurs when vesicle‐associated and target membrane‐associated SNARE s zipper into …

Accurate protein-folding transition-path statistics from a simple free-energy landscape

WM Jacobs, EI Shakhnovich - The Journal of Physical Chemistry …, 2018 - ACS Publications
A central goal of protein-folding theory is to predict the stochastic dynamics of transition
paths—the rare trajectories that transit between the folded and unfolded ensembles—using …

Helix–coil transition courses through multiple pathways and intermediates: fast kinetic measurements and dimensionality reduction

GS Jas, K Kuczera - The Journal of Physical Chemistry B, 2018 - ACS Publications
Nanosecond laser temperature jumps with tryptophan fluorescence detection and molecular
dynamics simulation with kinetic dimensionality reduction were used to study the helix–coil …

[HTML][HTML] The role of conformational entropy in the determination of structural-kinetic relationships for helix-coil transitions

JF Rudzinski, T Bereau - Computation, 2018 - mdpi.com
Coarse-grained molecular simulation models can provide significant insight into the
complex behavior of protein systems, but suffer from an inherently distorted description of …

Structural-kinetic-thermodynamic relationships identified from physics-based molecular simulation models

JF Rudzinski, T Bereau - The Journal of chemical physics, 2018 - pubs.aip.org
Coarse-grained molecular simulation models have provided immense, often general, insight
into the complex behavior of condensed-phase systems but suffer from a lost connection to …

Diverse Protein-Folding Pathways and Functions of β-Hairpins and β-Sheets

C Balusek, H Hwang, A Hazel, K Lundquist… - Quantitative Models for …, 2018 - Springer
One of the most common fundamental secondary-structure elements of proteins is the β-
sheet. Folding of β-sheets into various structures, eg, β-hairpins, β-barrels, and amyloids, is …

[PDF][PDF] Faltung und Entfaltung eines neu entwickelten lichtschaltbaren β-hairpin Modellpeptids und Untersuchung seiner hydrophoben Wechselwirkungen

SM Hofmann - 2018 - edoc.ub.uni-muenchen.de
Proteine sind in allen Zellen von Lebewesen enthalten und führen hier die verschiedensten
Funktionen des Lebens aus. Damit jedes Protein seine spezielle Aufgabe wahrnehmen …