138 related articles for article (PubMed ID: 27488241)
1. Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β.
Matute RA; Yoon H; Warshel A
Proteins; 2016 Nov; 84(11):1644-1657. PubMed ID: 27488241
[TBL] [Abstract][Full Text] [Related]
2. Analysis of proton wires in the enzyme active site suggests a mechanism of c-di-GMP hydrolysis by the EAL domain phosphodiesterases.
Grigorenko BL; Knyazeva MA; Nemukhin AV
Proteins; 2016 Nov; 84(11):1670-1680. PubMed ID: 27479508
[TBL] [Abstract][Full Text] [Related]
3. Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping.
Xiang Y; Warshel A
J Phys Chem B; 2008 Jan; 112(3):1007-15. PubMed ID: 18166038
[TBL] [Abstract][Full Text] [Related]
4. A quantum mechanical investigation of possible mechanisms for the nucleotidyl transfer reaction catalyzed by DNA polymerase beta.
Bojin MD; Schlick T
J Phys Chem B; 2007 Sep; 111(38):11244-52. PubMed ID: 17764165
[TBL] [Abstract][Full Text] [Related]
5. Proton-transfer reactions in reaction center of photosynthetic bacteria Rhodobacter sphaeroides.
Kaneko Y; Hayashi S; Ohmine I
J Phys Chem B; 2009 Jul; 113(26):8993-9003. PubMed ID: 19496556
[TBL] [Abstract][Full Text] [Related]
6. Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase.
Florián J; Goodman MF; Warshel A
J Am Chem Soc; 2003 Jul; 125(27):8163-77. PubMed ID: 12837086
[TBL] [Abstract][Full Text] [Related]
7. Amino acid substitution in the active site of DNA polymerase β explains the energy barrier of the nucleotidyl transfer reaction.
Batra VK; Perera L; Lin P; Shock DD; Beard WA; Pedersen LC; Pedersen LG; Wilson SH
J Am Chem Soc; 2013 May; 135(21):8078-88. PubMed ID: 23647366
[TBL] [Abstract][Full Text] [Related]
8. Energy analysis of chemistry for correct insertion by DNA polymerase beta.
Lin P; Pedersen LC; Batra VK; Beard WA; Wilson SH; Pedersen LG
Proc Natl Acad Sci U S A; 2006 Sep; 103(36):13294-9. PubMed ID: 16938895
[TBL] [Abstract][Full Text] [Related]
9. Hydrogen bonding and catalysis: a novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase.
Joshi MD; Sidhu G; Pot I; Brayer GD; Withers SG; McIntosh LP
J Mol Biol; 2000 May; 299(1):255-79. PubMed ID: 10860737
[TBL] [Abstract][Full Text] [Related]
10. The role of the putative catalytic base in the phosphoryl transfer reaction in a protein kinase: first-principles calculations.
Valiev M; Kawai R; Adams JA; Weare JH
J Am Chem Soc; 2003 Aug; 125(33):9926-7. PubMed ID: 12914447
[TBL] [Abstract][Full Text] [Related]
11. Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis.
Yoon H; Warshel A
Proteins; 2017 Aug; 85(8):1446-1453. PubMed ID: 28383109
[TBL] [Abstract][Full Text] [Related]
12. Uniform Free-Energy Profiles of the P-O Bond Formation and Cleavage Reactions Catalyzed by DNA Polymerases β and λ.
Klvaňa M; Bren U; Florián J
J Phys Chem B; 2016 Dec; 120(51):13017-13030. PubMed ID: 27992186
[TBL] [Abstract][Full Text] [Related]
13. Theoretical insights into the protonation states of active site cysteine and citrullination mechanism of Porphyromonas gingivalis peptidylarginine deiminase.
Zhao C; Ling B; Dong L; Liu Y
Proteins; 2017 Aug; 85(8):1518-1528. PubMed ID: 28486790
[TBL] [Abstract][Full Text] [Related]
14. DNA polymerase beta catalysis: are different mechanisms possible?
Alberts IL; Wang Y; Schlick T
J Am Chem Soc; 2007 Sep; 129(36):11100-10. PubMed ID: 17696533
[TBL] [Abstract][Full Text] [Related]
15. DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state.
Sucato CA; Upton TG; Kashemirov BA; Osuna J; Oertell K; Beard WA; Wilson SH; Florián J; Warshel A; McKenna CE; Goodman MF
Biochemistry; 2008 Jan; 47(3):870-9. PubMed ID: 18161950
[TBL] [Abstract][Full Text] [Related]
16. Characterization of the active site of DNA polymerase beta by molecular dynamics and quantum chemical calculation.
Rittenhouse RC; Apostoluk WK; Miller JH; Straatsma TP
Proteins; 2003 Nov; 53(3):667-82. PubMed ID: 14579358
[TBL] [Abstract][Full Text] [Related]
17. Comparative studies of the catalytic mechanisms of two chorismatases: CH-fkbo and CH-Hyg5.
Dong L; Liu Y
Proteins; 2017 Jun; 85(6):1146-1158. PubMed ID: 28263400
[TBL] [Abstract][Full Text] [Related]
18. Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol beta.
Xiang Y; Oelschlaeger P; Florián J; Goodman MF; Warshel A
Biochemistry; 2006 Jun; 45(23):7036-48. PubMed ID: 16752894
[TBL] [Abstract][Full Text] [Related]
19. Defective Nucleotide Release by DNA Polymerase β Mutator Variant E288K Is the Basis of Its Low Fidelity.
Mahmoud MM; Schechter A; Alnajjar KS; Huang J; Towle-Weicksel J; Eckenroth BE; Doublié S; Sweasy JB
Biochemistry; 2017 Oct; 56(41):5550-5559. PubMed ID: 28945359
[TBL] [Abstract][Full Text] [Related]
20. Mechanism of nucleotide incorporation in DNA polymerase beta.
Radhakrishnan R
Biochem Biophys Res Commun; 2006 Sep; 347(3):626-33. PubMed ID: 16842743
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]