Gene/Protein
Disease
Symptom
Drug
Enzyme
Compound
Pivot Concepts:
Gene/Protein
Disease
Symptom
Drug
Enzyme
Compound
Target Concepts:
Gene/Protein
Disease
Symptom
Drug
Enzyme
Compound
Query: EC:1.3.99.3 (
acyl-CoA dehydrogenase
)
1,425
document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)
A subject of great practical importance that has not received much attention is the question of the sensitivity of molecular dynamics simulations to the initial X-ray structure used to set up the calculation. We have found two cases in which seemingly similar structures lead to quite different results, and in this article we present a detailed analysis of these cases. The first case is
acyl-CoA dehydrogenase
, and the chief difference of the two structures is attributed to a slight shift in a backbone carbonyl that causes a key residue (the proton-abstracting base) to be in a bad conformation for reaction. The second case is xylose isomerase, and the chief difference of the two structures appears to be the ligand sphere of a
Mg2+
metal cofactor that plays an active role in catalysis.
...
PMID:Sensitivity of molecular dynamics simulations to the choice of the X-ray structure used to model an enzymatic reaction. 1532 78
