ArticleBiophysical journal2005
Effect of urea on peptide conformation in water: molecular dynamics and experimental characterization.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 145 citations in OpenAlex.
- Molecular mechanism of the common and opposing cosolvent effects of fluorinated alcohol and urea on a coiled coil protein.Protein science : a publication of the Protein Society · 2023Article
- Stability of Nanopeptides: Structure and Molecular Exchange of Self-assembled Peptide Fibers.ACS nano · 2023Article
- Adsorption of Mussel Protein on Polymer Antifouling Membranes: A Molecular Dynamics Study.Molecules (Basel, Switzerland) · 2021Article
- Article
- Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide.Journal of computer-aided molecular design · 2017Article
- Characterization of the Fishing Lines in Titiwai (=Arachnocampa luminosa Skuse, 1890) from New Zealand and Australia.PloS one · 2016Article
- Lack of Dependence of the Sizes of the Mesoscopic Protein Clusters on Electrostatics.Biophysical journal · 2015Article
- The structural basis of urea-induced protein unfolding in β-catenin.Acta crystallographica. Section D, Biological crystallography · 2014Article
- Structure and dynamics of urea/water mixtures investigated by vibrational spectroscopy and molecular dynamics simulation.The journal of physical chemistry. B · 2013Article
- Enzymes of urea synthesis are expressed at the ocular surface, and decreased urea in the tear fluid is associated with dry-eye syndrome.Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie · 2013Article
- Solute's perspective on how trimethylamine oxide, urea, and guanidine hydrochloride affect water's hydrogen bonding ability.The journal of physical chemistry. B · 2012Article
- Urea-Water Solvation Forces on Prion Structures.Journal of chemical theory and computation · 2012Article
- Unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations.PloS one · 2011Article
- Naturally occurring osmolytes modulate the nanomechanical properties of polycystic kidney disease domains.The Journal of biological chemistry · 2010Article
- Linking well-tempered metadynamics simulations with experiments.Biophysical journal · 2010Article
- Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: A simulation study consistent with experimental observations.Protein science : a publication of the Protein Society · 2009Article
- Effects of urea and acetic acid on the heme axial ligation structure of ferric myoglobin at very acidic pH.Archives of biochemistry and biophysics · 2009Article
- Urea impedes the hydrophobic collapse of partially unfolded proteins.Biophysical journal · 2009Article
- Urea, but not guanidinium, destabilizes proteins by forming hydrogen bonds to the peptide group.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Polar or apolar--the role of polarity for urea-induced protein denaturation.PLoS computational biology · 2008Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics simulations of a ribonuclease A C-peptide analog and a sequence variant were performed in water at 277 and 300 K and in 8 M urea to clarify the molecular denaturation mechanism induced by urea and the early events in protein unfolding. Spectroscopic characterization of the peptides showed that the C-peptide analog had a high alpha-helical content, which was not the case for the variant. In the simulations, interdependent side-chain interactions were responsible for the high stability of the alpha-helical C-peptide analog in the different solvents. The other peptide displayed alpha-helical unwinding that propagated cooperatively toward the N-terminal. The conformations sampled by the peptides depended on their sequence and on the solvent. The ability of water molecules to form hydrogen bonds to the peptide as well as the hydrogen bond lifetimes increased in the presence of urea, whereas water mobility was reduced near the peptide. Urea accumulated in excess around the peptide, to which it formed long-lived hydrogen bonds. The unfolding mechanisms induced by thermal denaturation and by urea are of a different nature, with urea-aqueous solutions providing a better peptide solvation than pure water. Our results suggest that the effect of urea on the chemical denaturation process involves both the direct and indirect mechanisms.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.