ArticleBiochemistry2015
Mapping allostery through computational glycine scanning and correlation analysis of residue-residue contacts.
Article in Biochemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed, 47 citations in OpenAlex.
- Molecular Behavior of Human β Defensin Type 3 Embedded in Different Model Lipid Membranes.Journal of chemical information and modeling · 2026Article
- Conformational transition of a polycationic hinge domain contributes to DNA binding.Biophysical chemistry · 2026Article
- BaNDyT: Bayesian Network modeling of molecular Dynamics Trajectories.bioRxiv : the preprint server for biology · 2024Article
- Bayesian network models identify cooperative GPCR:G protein interactions that contribute to G protein coupling.The Journal of biological chemistry · 2024Article
- Quantitative Assessment of Energetic Contributions of Residues in a SARS-CoV-2 Viral Enzyme/Nanobody Interface.Journal of chemical information and modeling · 2024Article
- Article
- Bayesian network models identify co-operative GPCR:G protein interactions that contribute to G protein coupling.bioRxiv : the preprint server for biology · 2023Article
- Sparse group selection and analysis of function-related residue for protein-state recognition.Journal of computational chemistry · 2022Article
- Statistical Analysis of Protein-Ligand Interaction Patterns in Nuclear Receptor RORγ.Frontiers in molecular biosciences · 2022Article
- Hidden electrostatic energy contributions define dynamic allosteric communications within p53 during molecular recognition.Biophysical journal · 2021Article
- Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering.International journal of molecular sciences · 2020Review
- Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework.Nucleic acids research · 2018Article
- Allosteric pathways in nuclear receptors - Potential targets for drug design.Pharmacology & therapeutics · 2018Review
- Article
- Hidden electrostatic basis of dynamic allostery in a PDZ domain.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- DNA-induced unfolding of the thyroid hormone receptor α A/B domain through allostery.FEBS open bio · 2017Article
- Ortho-Methylarylamines as Time-Dependent Inhibitors of Cytochrome P450 1A1 Enzyme.Drug metabolism letters · 2017Article
- The Promiscuity of Allosteric Regulation of Nuclear Receptors by Retinoid X Receptor.The journal of physical chemistry. B · 2016Article
- Dynamical network of residue-residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery.PLoS computational biology · 2016Article
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 allosteric mechanisms is essential for the physical control of molecular switches and downstream cellular responses. However, it is difficult to decode essential allosteric motions in a high-throughput scheme. A general two-pronged approach to performing automatic data reduction of simulation trajectories is presented here. The first step involves coarse-graining and identifying the most dynamic residue-residue contacts. The second step is performing principal component analysis of these contacts and extracting the large-scale collective motions expressed via these residue-residue contacts. We demonstrated the method using a protein complex of nuclear receptors. Using atomistic modeling and simulation, we examined the protein complex and a set of 18 glycine point mutations of residues that constitute the binding pocket of the ligand effector. The important motions that are responsible for the allostery are reported. In contrast to conventional induced-fit and lock-and-key binding mechanisms, a novel "frustrated-fit" binding mechanism of RXR for allosteric control was revealed.
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.