ArticleProceedings of the National Academy of Sciences of the United States of America2012
Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. 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.
- Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics.Journal of chemical theory and computation · 2021Article
- Understanding biochemical processes in the presence of sub-diffusive behavior of biomolecules in solution and living cells.Biophysical reviews · 2019Review
- From a Highly Disordered to a Metastable State: Uncovering Insights of α-Synuclein.ACS chemical neuroscience · 2018Article
- Single-Molecule Test for Markovianity of the Dynamics along a Reaction Coordinate.The journal of physical chemistry letters · 2018Article
- Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics.ACS chemical neuroscience · 2017Article
- 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
- 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
- Frequency response of a protein to local conformational perturbations.PLoS computational biology · 2013Article
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.
Funding
Abstract
Structural fluctuations of a protein are essential for a protein to function and fold. By using molecular dynamics (MD) simulations of the model α/β protein VA3 in its native state, the coupling between the main-chain (MC) motions [represented by coarse-grained dihedral angles (CGDAs) γ(n) based on four successive C(α) atoms (n - 1, n, n + 1, n + 2) along the amino acid sequence] and its side-chain (SC) motions [represented by CGDAs δ(n) formed by the virtual bond joining two consecutive C(α) atoms (n, n + 1) and the bonds joining these C(α) atoms to their respective C(β) atoms] was analyzed. The motions of SCs (δ(n)) and MC (γ(n)) over time occur on similar free-energy profiles and were found to be subdiffusive. The fluctuations of the SCs (δ(n)) and those of the MC (γ(n)) are generally poorly correlated on a ps time-scale with a correlation increasing with time to reach a maximum value at about 10 ns. This maximum value is close to the correlation between the δ(n)(t) and γ(n)(t) time-series extracted from the entire duration of the MD runs (400 ns) and varies significantly along the amino acid sequence. High correlations between the SC and MC motions [δ(t) and γ(t) time-series] were found only in flexible regions of the protein for a few residues which contribute the most to the slowest collective modes of the molecule. These results are a possible indication of the role of the flexible regions of proteins for the biological function and folding.
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.