Literature DB >> 16895324

Mechanisms and free energies of enzymatic reactions.

Jiali Gao1, Shuhua Ma, Dan T Major, Kwangho Nam, Jingzhi Pu, Donald G Truhlar.   

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Year:  2006        PMID： 16895324      PMCID： PMC4477011          DOI： 10.1021/cr050293k

Source DB:  PubMed          Journal:  Chem Rev        ISSN： 0009-2665            Impact factor:   60.622


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  153 in total

Review 1.  Binding energy, specificity, and enzymic catalysis: the circe effect.

Authors:  W P Jencks
Journal:  Adv Enzymol Relat Areas Mol Biol       Date:  1975

Review 2.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
Journal:  Adv Protein Chem       Date:  2003

3.  Hydride transfer catalyzed by xylose isomerase: mechanism and quantum effects.

Authors:  Mireia Garcia-Viloca; Cristóbal Alhambra; Donald G Truhlar; Jiali Gao
Journal:  J Comput Chem       Date:  2003-01-30       Impact factor: 3.376

4.  Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase.

Authors:  Kara E Ranaghan; Adrian J Mulholland
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Review 5.  Quantum-classical simulation methods for hydrogen transfer in enzymes: a case study of dihydrofolate reductase.

Authors:  Sharon Hammes-Schiffer
Journal:  Curr Opin Struct Biol       Date:  2004-04       Impact factor: 6.809

6.  Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions.

Authors:  Yan Zhao; Nathan E Schultz; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2006-03       Impact factor: 6.006

7.  The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase.

Authors:  Ian F Thorpe; Charles L Brooks
Journal:  Proteins       Date:  2004-11-15

8.  Effects of Arg90 Neutralization on the Enzyme-Catalyzed Rearrangement of Chorismate to Prephenate.

Authors:  Cristiano Ruch Werneck Guimarães; Marina Udier-Blagović; Ivan Tubert-Brohman; William L Jorgensen
Journal:  J Chem Theory Comput       Date:  2005-07       Impact factor: 6.006

9.  Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus.

Authors:  Ivan Tubert-Brohman; Cristiano Ruch Werneck Guimarães; William L Jorgensen
Journal:  J Chem Theory Comput       Date:  2005       Impact factor: 6.006

10.  Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction.

Authors:  Kara E Ranaghan; Lars Ridder; Borys Szefczyk; W Andrzej Sokalski; Johannes C Hermann; Adrian J Mulholland
Journal:  Org Biomol Chem       Date:  2004-03-03       Impact factor: 3.876
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  94 in total

Review 1.  Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions.

Authors:  Jingzhi Pu; Jiali Gao; Donald G Truhlar
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

2.  Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9.

Authors:  Shenglong Wang; Po Hu; Yingkai Zhang
Journal:  J Phys Chem B       Date:  2007-03-22       Impact factor: 2.991

3.  An exact formulation of hyperdynamics simulations.

Authors:  L Y Chen; N J M Horing
Journal:  J Chem Phys       Date:  2007-06-14       Impact factor: 3.488

4.  An interpretation of fluctuations in enzyme catalysis rate, spectral diffusion, and radiative component of lifetimes in terms of electric field fluctuations.

Authors:  Meher K Prakash; R A Marcus
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-02       Impact factor: 11.205

5.  Design-atom approach for the quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons.

Authors:  Chuanyun Xiao; Yingkai Zhang
Journal:  J Chem Phys       Date:  2007-09-28       Impact factor: 3.488

6.  Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis.

Authors:  Kwangho Nam; Jiali Gao; Darrin M York
Journal:  J Am Chem Soc       Date:  2008-03-18       Impact factor: 15.419

Review 7.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

8.  A remote mutation affects the hydride transfer by disrupting concerted protein motions in thymidylate synthase.

Authors:  Zhen Wang; Thelma Abeysinghe; Janet S Finer-Moore; Robert M Stroud; Amnon Kohen
Journal:  J Am Chem Soc       Date:  2012-10-15       Impact factor: 15.419

9.  Chemical Control in the Battle against Fidelity in Promiscuous Natural Product Biosynthesis: The Case of Trichodiene Synthase.

Authors:  Mudit Dixit; Michal Weitman; Jiali Gao; Dan T Major
Journal:  ACS Catal       Date:  2016-12-02       Impact factor: 13.084

10.  QM/MM free energy simulations: recent progress and challenges.

Authors:  Xiya Lu; Dong Fang; Shingo Ito; Yuko Okamoto; Victor Ovchinnikov; Qiang Cui
Journal:  Mol Simul       Date:  2016-07-05       Impact factor: 2.178
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