ArticleProceedings of the National Academy of Sciences of the United States of America2008
How main-chains of proteins explore the free-energy landscape in native states.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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
23 citing papers in PubMed, 55 citations in OpenAlex.
- Einstein Model of a Graph to Characterize Protein Folded/Unfolded States.Molecules (Basel, Switzerland) · 2023Article
- Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics.Journal of chemical theory and computation · 2021Article
- How Useful can the Voigt Profile be in Protein Folding Processes?The protein journal · 2021Article
- Phosphorylation Induces Conformational Rigidity at the C-Terminal Domain of AMPA Receptors.The journal of physical chemistry. B · 2019Article
- From a Highly Disordered to a Metastable State: Uncovering Insights of α-Synuclein.ACS chemical neuroscience · 2018Article
- Lysosomal enzyme tripeptidyl peptidase 1 destabilizes fibrillar Aβ by multiple endoproteolytic cleavages within the β-sheet domain.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics.ACS chemical neuroscience · 2017Article
- Article
- Intrinsic Localized Modes in Proteins.Scientific reports · 2015Article
- My 65 years in protein chemistry.Quarterly reviews of biophysics · 2015Review
- New Insights into Protein (Un)Folding Dynamics.The journal of physical chemistry letters · 2015Article
- Accounting for a mirror-image conformation as a subtle effect in protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Local vs global motions in protein folding.Journal of chemical theory and computation · 2013Article
- Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.PLoS computational biology · 2013Article
- Measurement of energy landscape roughness of folded and unfolded proteins.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion.Proteins · 2012Article
- Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Is protein folding sub-diffusive?PLoS computational biology · 2010Article
- Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an alpha/beta protein (crambin) and a beta-sheet polypeptide (BS2) in their "native" states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive C(alpha) atoms, increases as a power law of time, t(alpha), with an exponent alpha between 0.08 and 0.39 (alpha = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles.
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.