ArticlePloS one2013
Reaction trajectory revealed by a joint analysis of protein data bank.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- A Bright and Dynamic Future in Structural Biology.Advances in experimental medicine and biology · 2026Review
- Effects of allosteric effectors on oxygen binding to crystals of hemoglobin in the R-quaternary structure.Protein science : a publication of the Protein Society · 2025Article
- A computational strategy to improve the activity of tyrosine phenol-lyase for the synthesis of L-DOPA.Scientific reports · 2024Article
- The unique allosteric property of crocodilian haemoglobin elucidated by cryo-EM.Nature communications · 2024Article
- Article
- Deconvolution of dynamic heterogeneity in protein structure.Structural dynamics (Melville, N.Y.) · 2024Review
- The allosteric gating mechanism of the MthK channel.National science review · 2022Article
- Ultrafast Structural Changes Decomposed from Serial Crystallographic Data.The journal of physical chemistry letters · 2019Article
- Direct observation of conformational population shifts in crystalline human hemoglobin.The Journal of biological chemistry · 2017Article
- Molecular events during translocation and proofreading extracted from 200 static structures of DNA polymerase.Nucleic acids research · 2016Article
- Structural basis for cooperative oxygen binding and bracelet-assisted assembly of Lumbricus terrestris hemoglobin.Scientific reports · 2015Article
- Article
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1 author.
Funding
Abstract
Structural motions along a reaction pathway hold the secret about how a biological macromolecule functions. If each static structure were considered as a snapshot of the protein molecule in action, a large collection of structures would constitute a multidimensional conformational space of an enormous size. Here I present a joint analysis of hundreds of known structures of human hemoglobin in the Protein Data Bank. By applying singular value decomposition to distance matrices of these structures, I demonstrate that this large collection of structural snapshots, derived under a wide range of experimental conditions, arrange orderly along a reaction pathway. The structural motions along this extensive trajectory, including several helical transformations, arrive at a reverse engineered mechanism of the cooperative machinery (Ren, companion article), and shed light on pathological properties of the abnormal homotetrameric hemoglobins from α-thalassemia. This method of meta-analysis provides a general approach to structural dynamics based on static protein structures in this post genomics era.
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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.