ArticleBiophysical journal2005
Exploring the common dynamics of homologous proteins. Application to the globin family.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes.Proteins · 2025Article
- Reused Protein Segments Linked to Functional Dynamics.Molecular biology and evolution · 2024Article
- Non-Native Structures of Apomyoglobin and Apoleghemoglobin in Folding Intermediates Related to the Protein Misfolding.Molecules (Basel, Switzerland) · 2023Review
- What the protein data bank tells us about the evolutionary conservation of protein conformational diversity.Protein science : a publication of the Protein Society · 2022Article
- Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.Acta crystallographica. Section D, Structural biology · 2022Review
- A Comparative Evaluation of the Structural and Dynamic Properties of Insect Odorant Binding Proteins.Biomolecules · 2022Article
- Dynamical comparison between Drosha and Dicer reveals functional motion similarities and dissimilarities.PloS one · 2019Article
- Dynamics based clustering of globin family members.PloS one · 2018Article
- Selection on protein structure, interaction, and sequence.Protein science : a publication of the Protein Society · 2016Review
- Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes.PLoS computational biology · 2016Article
- Evolutionary Conserved Positions Define Protein Conformational Diversity.PLoS computational biology · 2016Article
- Using THz Spectroscopy, Evolutionary Network Analysis Methods, and MD Simulation to Map the Evolution of Allosteric Communication Pathways in c-Type Lysozymes.Molecular biology and evolution · 2016Article
- Adaptability of protein structures to enable functional interactions and evolutionary implications.Current opinion in structural biology · 2015Review
- Comparison of intrinsic dynamics of cytochrome p450 proteins using normal mode analysis.Protein science : a publication of the Protein Society · 2015Article
- Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution.PloS one · 2015Article
- WEBnm@ v2.0: Web server and services for comparing protein flexibility.BMC bioinformatics · 2014Article
- Comparison of the intrinsic dynamics of aminoacyl-tRNA synthetases.The protein journal · 2014Article
- A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.Journal of molecular biology · 2012Article
- Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics.PloS one · 2012Article
- Exploring the factors determining the dynamics of different protein folds.Protein science : a publication of the Protein Society · 2011Article
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Authors and funding
4 authors.
Funding
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Abstract
We present a procedure to explore the global dynamics shared between members of the same protein family. The method allows the comparison of patterns of vibrational motion obtained by Gaussian network model analysis. After the identification of collective coordinates that were conserved during evolution, we quantify the common dynamics within a family. Representative vectors that describe these dynamics are defined using a singular value decomposition approach. As a test case, the globin heme-binding family is considered. The two lowest normal modes are shown to be conserved within this family. Our results encourage the development of models for protein evolution that take into account the conservation of dynamical features.
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