[PDF][PDF] Spin relaxation enhancement confirms dominance of extended conformations in short alanine peptides
Mounting spectroscopic evidence indicates the presence of local order in unfolded proteins,
including polyprolineII (PII).[1–3] The data supporting this order rely on short-chain models …
including polyprolineII (PII).[1–3] The data supporting this order rely on short-chain models …
UV resonance Raman investigation of the conformations and lowest energy allowed electronic excited states of tri-and tetraalanine: charge transfer transitions
UV resonance Raman excitation profiles and Raman depolarization ratios were measured
for trialanine and tetraalanine between 198 and 210 nm. Excitation within the π→ π …
for trialanine and tetraalanine between 198 and 210 nm. Excitation within the π→ π …
Aggregation of polyalanine in a hydrophobic environment
The dimerization of polyalanine peptides in a hydrophobic environment was explored using
replica exchange molecular dynamics simulations. A nonpolar solvent (cyclohexane) was …
replica exchange molecular dynamics simulations. A nonpolar solvent (cyclohexane) was …
Local Backbone Preferences and Nearest‐Neighbor Effects in the Unfolded and Native States
After being synthesized in cells, nascent proteins perform a range of functions that are
typically associated with conformational changes. The largest conformational change …
typically associated with conformational changes. The largest conformational change …
Ionized Trilysine: A Model System for Understanding the Nonrandom Structure of Poly-l-lysine and Lysine-Containing Motifs in Proteins
DJ Verbaro, D Mathieu, SE Toal… - The Journal of …, 2012 - ACS Publications
It is now well-established that different amino acid residues can exhibit different
conformational distributions in the unfolded state of peptides and proteins. These …
conformational distributions in the unfolded state of peptides and proteins. These …
Conformations of phenylalanine in the tripeptides AFA and GFG probed by combining MD simulations with NMR, FTIR, polarized Raman, and VCD spectroscopy
Conformational properties of small, flexible peptides are a matter of ongoing interest since
they can be considered as models for unfolded proteins. However, the investigation of the …
they can be considered as models for unfolded proteins. However, the investigation of the …
PPII propensity of multiple-guest amino acids in a proline-rich environment
There has been considerable debate about the intrinsic PPII propensity of amino acid
residues in denatured polypeptides. Experimentally, this scale is based on the behavior of …
residues in denatured polypeptides. Experimentally, this scale is based on the behavior of …
Homochiral stereochemistry: the missing link of structure to energetics in protein folding
The notion is tested that homochiral stereochemistry being ubiquitous to protein structure
could be critical to protein folding as well, causing it to become frustrated energetically …
could be critical to protein folding as well, causing it to become frustrated energetically …
Scrutiny of chain-length and N-terminal effects in α-helix folding: a molecular dynamics study on polyalanine peptides
Protein folding remains an unsolved problem as main-chain, side-chain, and solvent
interactions remain entangled and have been hard to resolve. Polyalanines are promising …
interactions remain entangled and have been hard to resolve. Polyalanines are promising …
Comparing the ability of enhanced sampling molecular dynamics methods to reproduce the behavior of fluorescent labels on proteins
K Walczewska-Szewc, E Deplazes… - Journal of Chemical …, 2015 - ACS Publications
Adequately sampling the large number of conformations accessible to proteins and other
macromolecules is one of the central challenges in molecular dynamics (MD) simulations; …
macromolecules is one of the central challenges in molecular dynamics (MD) simulations; …