Insights from molecular dynamics simulations for computational protein design

MC Childers, V Daggett - Molecular systems design & engineering, 2017 - pubs.rsc.org
A grand challenge in the field of structural biology is to design and engineer proteins that
exhibit targeted functions. Although much success on this front has been achieved, design …

The role of α-sheet structure in amyloidogenesis: Characterization and implications

T Prosswimmer, V Daggett - Open Biology, 2022 - royalsocietypublishing.org
Amyloid diseases are linked to protein misfolding whereby the amyloidogenic protein
undergoes a conformational change, aggregates and eventually forms amyloid fibrils. While …

Tuning the flexibility of glycine-serine linkers to allow rational design of multidomain proteins

M Van Rosmalen, M Krom, M Merkx - Biochemistry, 2017 - ACS Publications
Flexible polypeptide linkers composed of glycine and serine are important components of
engineered multidomain proteins. We have previously shown that the conformational …

[HTML][HTML] Using chirality to probe the conformational dynamics and assembly of intrinsically disordered amyloid proteins

JA Raskatov, DB Teplow - Scientific reports, 2017 - nature.com
Intrinsically disordered protein (IDP) conformers occupy large regions of conformational
space and display relatively flat energy surfaces. Amyloid-forming IDPs, unlike natively …

Designed α-sheet peptides suppress amyloid formation in Staphylococcus aureus biofilms

A Bleem, R Francisco, JD Bryers… - npj Biofilms and …, 2017 - nature.com
Nosocomial infections affect hundreds of millions of patients worldwide each year, and~
60% of these infections are associated with biofilm formation on an implanted medical …

Exploring the self-assembly mechanisms of wheat gluten polypeptide hydrogels: Synthesis and characterization

J Cao, G Fan, B Lu - Journal of Food Engineering, 2025 - Elsevier
The purpose of this study was to demonstrate a mild enzymatic method for the large-scale
production of nano-scale self-assembled peptide hydrogels (WGP-M, average molecular …

The design of functional proteins using tensorized energy calculations

K Maksymenko, A Maurer, N Aghaallaei, C Barry… - Cell Reports …, 2023 - cell.com
In protein design, the energy associated with a huge number of sequence-conformer
perturbations has to be routinely estimated. Hence, enhancing the throughput and accuracy …

Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective

PI Maxwell, PLA Popelier - Journal of computational chemistry, 2017 - Wiley Online Library
Accurate description of the intrinsic preferences of amino acids is important to consider
when developing a biomolecular force field. In this study, we use a modern energy …

Sortase A transpeptidation produces seamless, unbranched biotinylated nanobodies for multivalent and multifunctional applications

EM Obeng, DL Steer, AJ Fulcher, KM Wagstaff - Nanoscale Advances, 2023 - pubs.rsc.org
Exploitation of the biotin–streptavidin interaction for advanced protein engineering is used in
many bio-nanotechnology applications. As such, researchers have used diverse techniques …

The hot sites of α-synuclein in amyloid fibril formation

A Khammari, SS Arab, MR Ejtehadi - Scientific Reports, 2020 - nature.com
The role of alpha-synuclein (αS) amyloid fibrillation has been recognized in various
neurological diseases including Parkinson's Disease (PD). In early stages, fibrillation occurs …