PMID- 23901785
OWN - NLM
STAT- MEDLINE
DCOM- 20131126
LR  - 20211021
IS  - 1520-4995 (Electronic)
IS  - 0006-2960 (Print)
IS  - 0006-2960 (Linking)
VI  - 52
IP  - 33
DP  - 2013 Aug 20
TI  - Predicting enzyme-substrate specificity with QM/MM methods: a case study of the 
      stereospecificity of (D)-glucarate dehydratase.
PG  - 5511-3
LID - 10.1021/bi400546j [doi]
AB  - The stereospecificity of d-glucarate dehydratase (GlucD) is explored by QM/MM 
      calculations. Both the substrate binding and the chemical steps of GlucD 
      contribute to substrate specificity. Although the identification of transition 
      states remains computationally intensive, we suggest that QM/MM computations on 
      ground states or intermediates can capture aspects of specificity that cannot be 
      obtained using docking or molecular mechanics methods.
FAU - Tian, Boxue
AU  - Tian B
AD  - School of Chemistry, National University of Ireland, Galway, Galway, Ireland.
FAU - Wallrapp, Frank
AU  - Wallrapp F
FAU - Kalyanaraman, Chakrapani
AU  - Kalyanaraman C
FAU - Zhao, Suwen
AU  - Zhao S
FAU - Eriksson, Leif A
AU  - Eriksson LA
FAU - Jacobson, Matthew P
AU  - Jacobson MP
LA  - eng
GR  - U54 GM093342/GM/NIGMS NIH HHS/United States
GR  - U54-GM093342/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20130809
PL  - United States
TA  - Biochemistry
JT  - Biochemistry
JID - 0370623
RN  - 0 (Adipates)
RN  - 0 (mannaric acid)
RN  - EC 4.2.1.- (Hydro-Lyases)
RN  - EC 4.2.1.40 (glucarate dehydratase)
RN  - QLZ991V4A2 (Glucaric Acid)
SB  - IM
MH  - Adipates/chemistry/metabolism
MH  - Biocatalysis
MH  - Glucaric Acid/*chemistry/metabolism
MH  - Hydro-Lyases/*chemistry/metabolism
MH  - Models, Chemical
MH  - Models, Molecular
MH  - *Molecular Dynamics Simulation
MH  - Molecular Structure
MH  - Protein Binding
MH  - Protein Structure, Tertiary
MH  - *Quantum Theory
MH  - Stereoisomerism
MH  - Substrate Specificity
MH  - Thermodynamics
PMC - PMC3964877
MID - NIHMS561629
EDAT- 2013/08/02 06:00
MHDA- 2013/12/16 06:00
PMCR- 2014/08/20
CRDT- 2013/08/02 06:00
PHST- 2013/08/02 06:00 [entrez]
PHST- 2013/08/02 06:00 [pubmed]
PHST- 2013/12/16 06:00 [medline]
PHST- 2014/08/20 00:00 [pmc-release]
AID - 10.1021/bi400546j [doi]
PST - ppublish
SO  - Biochemistry. 2013 Aug 20;52(33):5511-3. doi: 10.1021/bi400546j. Epub 2013 Aug 9.