Linked Life Data

19862811

Source:http://linkedlifedata.com/resource/pubmed/id/19862811

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
6
pubmed:dateCreated
2010-3-18
pubmed:abstractText
A method for computational design of protein-ligand interactions is implemented and tested on the asparaginyl- and aspartyl-tRNA synthetase enzymes (AsnRS, AspRS). The substrate specificity of these enzymes is crucial for the accurate translation of the genetic code. The method relies on a molecular mechanics energy function and a simple, continuum electrostatic, implicit solvent model. As test calculations, we first compute AspRS-substrate binding free energy changes due to nine point mutations, for which experimental data are available; we also perform large-scale redesign of the entire active site of each enzyme (40 amino acids) and compare to experimental sequences. We then apply the method to engineer an increased binding of aspartyl-adenylate (AspAMP) into AsnRS. Mutants are obtained using several directed evolution protocols, where four or five amino acid positions in the active site are randomized. Promising mutants are subjected to molecular dynamics simulations; Poisson-Boltzmann calculations provide an estimate of the corresponding, AspAMP, binding free energy changes, relative to the native AsnRS. Several of the mutants are predicted to have an inverted binding specificity, preferring to bind AspAMP rather than the natural substrate, AsnAMP. The computed binding affinities are significantly weaker than the native, AsnRS:AsnAMP affinity, and in most cases, the active site structure is significantly changed, compared to the native complex. This almost certainly precludes catalytic activity. One of the designed sequences has a higher affinity and more native-like structure and may represent a valid candidate for Asp activity.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Apr
pubmed:issn
1096-987X
pubmed:author
pubmed:copyrightInfo
2009 Wiley Periodicals, Inc.
pubmed:issnType
Electronic
pubmed:day
30
pubmed:volume
31
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1273-86
pubmed:meshHeading
pubmed:year
2010
pubmed:articleTitle
Computational design of protein-ligand binding: modifying the specificity of asparaginyl-tRNA synthetase.
pubmed:affiliation
Laboratoire de Biochimie, Department of Biology, UMR CNRS 7654, Ecole Polytechnique, 91128 Palaiseau, France.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't