ArticlePLoS computational biology2013
Collective dynamics underlying allosteric transitions in hemoglobin.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 35 citations in OpenAlex.
- Mapping the Binding Landscape of Allosteric Inhibitor G6PDi-1 on Human G6PD.The journal of physical chemistry letters · 2026Article
- Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles.Computational and structural biotechnology journal · 2023Article
- Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs.Journal of chemical information and modeling · 2022Article
- Quaternary Structure Transitions of Human Hemoglobin: An Atomic-Level View of the Functional Intermediate States.Journal of chemical information and modeling · 2021Article
- Exposing the distinctive modular behavior of β-strands and α-helices in folded proteins.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'.eLife · 2019Article
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- Identifying coupled clusters of allostery participants through chemical shift perturbations.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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- Comparative Study of Elastic Network Model and Protein Contact Network for Protein Complexes: The Hemoglobin Case.BioMed research international · 2017Article
- The Dynamic Behavior of the P2XBiophysical journal · 2016Article
- Induced Fit in Protein Multimerization: The HFBI Case.PLoS computational biology · 2016Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hemoglobin is the prototypic allosteric protein. Still, its molecular allosteric mechanism is not fully understood. To elucidate the mechanism of cooperativity on an atomistic level, we developed a novel computational technique to analyse the coupling of tertiary and quaternary motions. From Molecular Dynamics simulations showing spontaneous quaternary transitions, we separated the transition trajectories into two orthogonal sets of motions: one consisting of intra-chain motions only (referred to as tertiary-only) and one consisting of global inter-chain motions only (referred to as quaternary-only). The two underlying subspaces are orthogonal by construction and their direct sum is the space of full motions. Using Functional Mode Analysis, we were able to identify a collective coordinate within the tertiary-only subspace that is correlated to the most dominant motion within the quaternary-only motions, hence providing direct insight into the allosteric coupling mechanism between tertiary and quaternary conformation changes. This coupling-motion is substantially different from tertiary structure changes between the crystallographic structures of the T- and R-state. We found that hemoglobin's allosteric mechanism of communication between subunits is equally based on hydrogen bonds and steric interactions. In addition, we were able to affect the T-to-R transition rates by choosing different histidine protonation states, thereby providing a possible atomistic explanation for the Bohr effect.
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