Evolutionary and Functional Relationships in the Truncated Hemoglobin Family

PLoS Computational Biology
Juan P BustamanteMarcelo A Martí

Abstract

Predicting function from sequence is an important goal in current biological research, and although, broad functional assignment is possible when a protein is assigned to a family, predicting functional specificity with accuracy is not straightforward. If function is provided by key structural properties and the relevant properties can be computed using the sequence as the starting point, it should in principle be possible to predict function in detail. The truncated hemoglobin family presents an interesting benchmark study due to their ubiquity, sequence diversity in the context of a conserved fold and the number of characterized members. Their functions are tightly related to O2 affinity and reactivity, as determined by the association and dissociation rate constants, both of which can be predicted and analyzed using in-silico based tools. In the present work we have applied a strategy, which combines homology modeling with molecular based energy calculations, to predict and analyze function of all known truncated hemoglobins in an evolutionary context. Our results show that truncated hemoglobins present conserved family features, but that its structure is flexible enough to allow the switch from high to low affinity in a few...Continue Reading

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Citations

May 7, 2016·Bioinformatics·Juan P BustamanteLeonardo Boechi
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Mar 29, 2020·Journal of Inorganic Biochemistry·Darya Marchany-RiveraJuan López-Garriga
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Methods Mentioned

BETA
in-silico methods
X-ray

Software Mentioned

ProtTest
AMBER12
CD
HMMER profiling
AMBER
BLAST
MM
BIONJ
SIESTA
hmmsearch

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