ArticleProteins2009
The energy profiles of atomic conformational transition intermediates of adenylate kinase.
Article in Proteins, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Towards design of drugs and delivery systems with the Martini coarse-grained model.QRB discovery · 2022Review
- Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC.Molecules (Basel, Switzerland) · 2021Article
- ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths.Journal of computer-aided molecular design · 2019Article
- Detecting intermediate protein conformations using algebraic topology.BMC bioinformatics · 2017Article
- ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution.Journal of chemical theory and computation · 2016Article
- Article
- Features of large hinge-bending conformational transitions. Prediction of closed structure from open state.Biophysical journal · 2014Article
- Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods.BMC structural biology · 2013Article
- Elastic network normal modes provide a basis for protein structure refinement.The Journal of chemical physics · 2012Article
- Protein folding pathways and state transitions described by classical equations of motion of an elastic network model.Protein science : a publication of the Protein Society · 2010Article
- Models to Approximate the Motions of Protein Loops.Journal of chemical theory and computation · 2010Article
- Tracing conformational changes in proteins.BMC structural biology · 2010Article
- Structural dynamics of bio-macromolecules by NMR: the slowly relaxing local structure approach.Progress in nuclear magnetic resonance spectroscopy · 2010Review
- Moving beyond static snapshots: Protein dynamics and the Protein Data Bank.The Journal of biological chemistryReview
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Authors and funding
4 authors.
Funding
Abstract
The elastic network interpolation (ENI) (Kim et al., Biophys J 2002;83:1620-1630) is a computationally efficient and physically realistic method to generate conformational transition intermediates between two forms of a given protein. However it can be asked whether these calculated conformations provide good representatives for these intermediates. In this study, we use ENI to generate conformational transition intermediates between the open form and the closed form of adenylate kinase (AK). Based on C(alpha)-only intermediates, we construct atomic intermediates by grafting all the atoms of known AK structures onto the C(alpha) atoms and then perform CHARMM energy minimization to remove steric conflicts and optimize these intermediate structures. We compare the energy profiles for all intermediates from both the CHARMM force-field and from knowledge-based energy functions. We find that the CHARMM energies can successfully capture the two energy minima representing the open AK and closed AK forms, while the energies computed from the knowledge-based energy functions can detect the local energy minimum representing the closed AK form and show some general features of the transition pathway with a somewhat similar energy profile as the CHARMM energies. The combinatorial extension structural alignment (Shindyalov et al., 1998;11:739-747) and the k-means clustering algorithm are then used to show that known PDB structures closely resemble computed intermediates along the transition pathway.
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