Results 51 to 60 of about 1,516,213 (305)

De novo ß-hairpin design using a residue-basedphysicochemical property landscape [PDF]

Structural Dynamics
De novo peptide design is a rapidly evolving field with significant promise for applications in both biological and biomedical sectors. Traditional peptide design methods often rely on sequence homology, which is limited to evolutionarily related ...
Vardhan Satalkar, Julie Mitchell, Mathhew Torres   +2 more
doaj   +1 more source

Swapping the Positions in a Cross-Strand Lateral Ion-Pairing Interaction between Ammonium- and Carboxylate-Containing Residues in a β-Hairpin

Molecules, 2021
Cross-strand lateral ion-pairing interactions are important for antiparallel β-sheet stability. Statistical studies suggested that swapping the position of cross-strand lateral residues should not significantly affect the interaction.
Cheng-Hsin Huang, Tong Wai Wong, Chen-Hsu Yu, Jing-Yuan Chang, Shing-Jong Huang, Shou-Ling Huang, Richard P. Cheng   +6 more
doaj   +1 more source

Evaluating force field accuracy with long-time simulations of a tryptophan zipper peptide

, 2010
We have combined a custom implementation of the fast multiple-time-stepping LN integrator with parallel tempering to explore folding properties of small peptides in implicit solvent on the time scale of microseconds.
Cox, Daniel L., Hayre, Natha R., Singh, Rajiv R. P.   +2 more
core   +1 more source

Assessment and Optimization of Collective Variables for Protein Conformational Landscape: GB1 β-hairpin as a Case Study

bioRxiv, 2018
Collective variables (CV), when chosen judiciously, can play an important role in recognizing rate-limiting processes and rare events in any biomolecular systems.
Navjeet Ahalawat, Jagannath Mondal
semanticscholar   +1 more source

Sequence-based identification of amyloidogenic β-hairpins reveals a prostatic acid phosphatase fragment promoting semen amyloid formation

Computational and Structural Biotechnology Journal
β-Structure-rich amyloid fibrils are hallmarks of several diseases, including Alzheimer’s (AD), Parkinson’s (PD), and type 2 diabetes (T2D). While amyloid fibrils typically consist of parallel β-sheets, the anti-parallel β-hairpin is a structural motif ...
Laetitia F. Heid, Emil Dandanell Agerschou, Asuka A. Orr, Tatsiana Kupreichyk, Walfried Schneider, Michael M. Wördehoff, Melanie Schwarten, Dieter Willbold, Phanourios Tamamis, Matthias Stoldt, Wolfgang Hoyer   +10 more
doaj   +1 more source

Periodic force induced stabilization or destabilization of the denatured state of a protein

, 2012
We have studied the effects of an external sinusoidal force in protein folding kinetics. The externally applied force field acts on the each amino acid residues of polypeptide chains.
Bidhan Chandra Bag, Hansen J. P., Liu D.-S., Mai Suan Li, Pulak Kumar Ghosh   +4 more
core   +1 more source

Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics [PDF]

, 2013
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of ...
Gront, Dominik, Kmiecik, Sebastian, Kolinski, Andrzej, Kouza, Maksim, Wabik, Jacek   +4 more
core   +3 more sources

Structure-Dependent Immune Modulatory Activity of Protegrin-1 Analogs

Antibiotics, 2014
Protegrins are porcine antimicrobial peptides (AMPs) that belong to the cathelicidin family of host defense peptides. Protegrin-1 (PG-1), the most investigated member of the protegrin family, is an arginine-rich peptide consisting of 18 amino acid ...
Susu M. Zughaier, Pavel Svoboda, Jan Pohl   +2 more
doaj   +1 more source

Structural Characterization of Rat Galectin-5, an N-Tailed Monomeric Proto-Type-like Galectin

Biomolecules, 2021
Galectins are multi-purpose effectors acting via interactions with distinct counterreceptors based on protein-glycan/protein recognition. These processes are emerging to involve several regions on the protein so that the availability of a detailed ...
Federico M. Ruiz, Francisco J. Medrano, Anna-Kristin Ludwig, Herbert Kaltner, Nadezhda V. Shilova, Nicolai V. Bovin, Hans-Joachim Gabius, Antonio Romero   +7 more
doaj   +1 more source

Electroactive Liquid Crystal Elastomers as Soft Actuators

Advanced Functional Materials, EarlyView.
Electroactive liquid crystal elastomers (eLCEs) can be actuated via electromechanical, electrochemical, or electrothermal effects. a) Electromechanical effects include Maxwell stress, electrostriction, and the electroclinic effect. b) Electrochemical effects arise from electrode redox reactions.
Yakui Deng, Min‐Hui Li
wiley   +1 more source