ArticleBiophysical journal2007
Coarse-grained free energy functions for studying protein conformational changes: a double-well network model.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 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
60 citing papers in PubMed, 139 citations in OpenAlex.
- Allostery can convert binding free energies into concerted domain motions in enzymes.Nature communications · 2024Article
- Whispering-Gallery Mode Optoplasmonic Microcavities: From Advanced Single-Molecule Sensors and Microlasers to Applications in Synthetic Biology.ACS photonics · 2024Review
- Statistical Mechanical Design Principles for Coarse-Grained Interactions across Different Conformational Free Energy Surfaces.The journal of physical chemistry letters · 2023Article
- Tracking the ATP-binding response in adenylate kinase in real time.Science advances · 2021Article
- Exploring the landscape of model representations.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Binding-Induced Conformational Changes Involved in Sliding Clamp PCNA and DNA Polymerase DPO4.iScience · 2020Article
- When Stiffness Matters: Mechanosensing in Heart Development and Disease.Frontiers in cell and developmental biology · 2020Review
- Multiconfigurational Coarse-Grained Molecular Dynamics.Journal of chemical theory and computation · 2019Article
- Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.International journal of molecular sciences · 2018Review
- High aspect ratio nanotubes assembled from macrocyclic iminium salts.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Quantifying the Intrinsic Conformation Energy Landscape Topography of Proteins with Large-Scale Open-Closed Transition.ACS central science · 2018Article
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
- Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Fast Protein Translation Can Promote Co- and Posttranslational Folding of Misfolding-Prone Proteins.Biophysical journal · 2017Article
- A Rough Energy Landscape to Describe Surface-Linked Antibody and Antigen Bond Formation.Scientific reports · 2016Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits.The Journal of chemical physics · 2015Article
- Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case.Biophysical journal · 2015Article
- Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field.Journal of computer-aided molecular design · 2015Article
- Molecular investigations into the mechanics of a muscle anchoring complex.Biophysical journal · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
In this work, a double-well network model (DWNM) is presented for generating a coarse-grained free energy function that can be used to study the transition between reference conformational states of a protein molecule. Compared to earlier work that uses a single, multidimensional double-well potential to connect two conformational states, the DWNM uses a set of interconnected double-well potentials for this purpose. The DWNM free energy function has multiple intermediate states and saddle points, and is hence a "rough" free energy landscape. In this implementation of the DWNM, the free energy function is reduced to an elastic-network model representation near the two reference states. The effects of free energy function roughness on the reaction pathways of protein conformational change is demonstrated by applying the DWNM to the conformational changes of two protein systems: the coil-to-helix transition of the DB-loop in G-actin and the open-to-closed transition of adenylate kinase. In both systems, the rough free energy function of the DWNM leads to the identification of distinct minimum free energy paths connecting two conformational states. These results indicate that while the elastic-network model captures the low-frequency vibrational motions of a protein, the roughness in the free energy function introduced by the DWNM can be used to characterize the transition mechanism between protein conformations.
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.