From peptides to peptidomimetics: a strategy based on the structural features of cyclopropane

A Mizuno, K Matsui, S Shuto - Chemistry–A European Journal, 2017 - Wiley Online Library
Peptidomimetics, non‐natural mimicries of bioactive peptides, comprise an important class
of drug molecules. The essence of the peptidomimetic design is to mimic the key …

Malleability of protein folding pathways: a simple reason for complex behaviour

MO Lindberg, M Oliveberg - Current opinion in structural biology, 2007 - Elsevier
Although the structures of native proteins are generally unique, the pathways by which they
form are often free to vary. Some proteins fold by a multitude of different pathways, whereas …

Alternative low-populated conformations prompt phase transitions in polyalanine repeat expansions

R Antón, MÁ Treviño, D Pantoja-Uceda, S Félix… - Nature …, 2024 - nature.com
Abnormal trinucleotide repeat expansions alter protein conformation causing malfunction
and contribute to a significant number of incurable human diseases. Scarce structural …

Assignment of PolyProline II conformation and analysis of sequence–structure relationship

Y Mansiaux, AP Joseph, JC Gelly, AG de Brevern - PloS one, 2011 - journals.plos.org
Background Secondary structures are elements of great importance in structural biology,
biochemistry and bioinformatics. They are broadly composed of two repetitive structures …

Arginine-assisted solubilization system for drug substances: solubility experiment and simulation

A Hirano, T Kameda, T Arakawa… - The Journal of Physical …, 2010 - ACS Publications
The poor aqueous solubility of drug substances hampers their broader applications. This
paper describes a de novo strategy to increase the aqueous solubility of drug substances …

Residual structure in the denatured state of the fast-folding UBA (1) domain from the human DNA excision repair protein HHR23A

DC Becht, MJ Leavens, B Zeng, MT Rothfuss… - Biochemistry, 2022 - ACS Publications
The structure of the first ubiquitin-associated domain from HHR23A, UBA (1), was
determined by X-ray crystallography at a 1.60 Å resolution, and its stability, folding kinetics …

Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water

J Ikebe, K Umezawa, N Kamiya… - Journal of …, 2011 - Wiley Online Library
Trivial trajectory parallelization of multicanonical molecular dynamics (TTP‐McMD) explores
the conformational space of a biological system with multiple short runs of McMD starting …

Length-dependent aggregation of uninterrupted polyalanine peptides

JP Bernacki, RM Murphy - Biochemistry, 2011 - ACS Publications
Polyalanine (polyA) is the third-most prevalent homopeptide repeat in eukaryotes, behind
polyglutamine and polyasparagine. Abnormal expansion of the polyA repeat is linked to at …

Comparison between empirical protein force fields for the simulation of the adsorption behavior of structured LK peptides on functionalized surfaces

G Collier, NA Vellore, JA Yancey, SJ Stuart… - Biointerphases, 2012 - pubs.aip.org
All-atom empirical molecular mechanics protein force fields, which have been developed to
represent the energetics of peptide folding behavior in aqueous solution, have not been …

A comparative molecular dynamics analysis of the amyloid β-peptide in a lipid bilayer

JA Lemkul, DR Bevan - Archives of biochemistry and biophysics, 2008 - Elsevier
Because the amyloid β-peptide (Aβ) functions as approximately half of the transmembrane
domain of the amyloid precursor protein and interaction of Aβ with membranes is proposed …