ArticleBiophysical journal2010
Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed, 44 citations in OpenAlex.
- Association analysis and in silico functional predictions of RMDN2 variants in chickens.Animal bioscience · 2026Article
- Cancer-associated TRF1 mutations alter PARP1 interaction dynamics: an in silico study.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Short disordered protein segment regulates cross-species transmission of a yeast prion.Nature chemical biology · 2020Article
- Protein structure predictions by enhanced conformational sampling methods.Biophysics and physicobiology · 2019Review
- Solvent-Driven Dynamical Crossover in the Phenylalanine Side-Chain from the Hydrophobic Core of Amyloid Fibrils Detected byThe journal of physical chemistry. B · 2017Article
- Flexible Proteins at the Origin of Life.Life (Basel, Switzerland) · 2017Article
- Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding.PLoS computational biology · 2015Article
- Article
- Mathematical and computational modeling in biology at multiple scales.Theoretical biology & medical modelling · 2014Review
- Following easy slope paths on a free energy landscape: the case study of the Trp-cage folding mechanism.Biophysical journal · 2013Article
- Reduced native state stability in crowded cellular environment due to protein-protein interactions.Journal of the American Chemical Society · 2013Article
- Conformational flexibility of N-glycans in solution studied by REMD simulations.Biophysical reviews · 2012Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite its small size, chicken villin headpiece subdomain HP36 folds into the native structure with a stable hydrophobic core within several microseconds. How such a small protein keeps up its conformational stability and fast folding in solution is an important issue for understanding molecular mechanisms of protein folding. In this study, we performed multicanonical replica-exchange simulations of HP36 in explicit water, starting from a fully extended conformation. We observed at least five events of HP36 folding into nativelike conformations. The smallest backbone root mean-square deviation from the crystal structure was 1.1 A. In the nativelike conformations, the stably formed hydrophobic core was fully dehydrated. Statistical analyses of the simulation trajectories show the following sequential events in folding of HP36: 1), Helix 3 is formed at the earliest stage; 2), the backbone and the side chains near the loop between Helices 2 and 3 take nativelike conformations; and 3), the side-chain packing at the hydrophobic core and the dehydration of the core side chains take place simultaneously at the later stage of folding. This sequence suggests that the initial folding nucleus is not necessarily the same as the hydrophobic core, consistent with a recent experimental phi-value analysis.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.